The main goal for this part of the adventure is for the players to locate a lost/crashed sky ship (not a very large one mind you). I do not want this to be the end of the campaign. 
The help I need is about when they actually reach the sky ship. I don't want this to be a game breaking thing by them keeping it. I was thinking they would need to use it to travel to another land where they are needed (there may be natives of that land, living in the non working sky ship as part of the whole adventure is finding the power sources needed to power it)..... Or it could be unflyable at all and they could use it as a base of operations?.... Or another faction had been trailing them and eventually attacks and steals the sky ship??....Or....I am completely open to suggestions. 

hmm... skyships are pretty awesome so I can certainly see the appeal.

How large of a plothook do you want this to be? You could have the skyship be some ancient thing, preserved in sand/bog/ice/dry-dock/ whatever fits your setting, with some crystal-driven energy source which allows it to fly. The energy source is dormant, and there are legends which tell of an ancient civilization of great power (think atlantis) who used these crystals, and that they were deactivated by those jealous of the advanced people. You give your adventurers a chance to reactivate this power to fuel their sky ship by means of a quest, and when they do so, the crystals re-energise - and an entire city bursts out of the sand/sea/ice and floats upwards on the power of the crystals upon which it is built.

The city is devoid of life but contains a multitude of ancient automatons which have returned to functionality now the crystal is re-energized. The adventurers can access it with their skyship, but might get shot down when flying over - leading to a dungeon crawl through a dead city whose past they can unravel. Perhaps after they land they activate the cities defences, destroying their skyship and preventing anyone from getting in or out. You could create all sorts of treasure, and use a lot of constructs for a really cool game. Perhaps the city is also powering up a doomsday weapon which was the whole reason their enemies shut them down in the first place, and the adventurers have to deactivate it in time. It would certainly be a cool way to continue the campaign if the "BBEG" was just an accident caused by the party wanting a skyship! Maybe you can throw in an extra double-bluff that the automatons are moving for war, and the "doomsday weapon" was built to save the rest of the world from their rogue constructs? I think the backstory has legs!

I know it might not be exactly what you are looking for but what if you did three sessions where they find the pieces missing and then continued the rest of the campaign on the ship. Here is my idea... What if when they actually got the ship to work and explored it a little better they would find a Weird machine and by accident activate it and then were teleported to another plane of existence were there is no land but floating Islands big and small so that they can use it that way. They concept is like hoping from one place to another and trying to navigate themselves through this giant plane full of floating islands and maybe other pirate floating ships so that they can do something like ship Vs ship combat in midair while they are almost crushing to a moving floating island and then basically trying to find and destroy the source of this piracy. This is a smart way to throw some wandering merchant ships and maybe floating towns so that it can be more interesting that just carts with barrels inside a normal city. I don't know if you like it I just came up with it hope it helps...  

These are both great ideas and suggestions that I m sure I can work with. Thank you very much

Ok this is what I am going to do. (this part I had already hashed out before I asked my question) The players are searching for 5 crystals that will power the sky ship. 
The ship is in no condition to fly. Constructs power up as each crystal is put into it's cradle. The number of constructs, (I still have to determined this) don't attack, but start right away to repair the ship and any weapons on board (I want there to be a city leveling weapon/s and I am open to ideas on this. The ship and the constructs were sent on a mission to destroy Faerun (from a neighbouring world). 

Other than the PCs seeing the constructs fire the weapon, how could they discover this?
What could the weapon be? A series of super sized canons? A machine that opens portals from the nine realms, to allow many monsters to enter a city at once?

help 

If you want them to fly it just once, give it one trip's worth of some rare and very difficult to find fuel.

For discovering the city-levelling weapons, I'd be looking to keep it simple and have the weapons cause a huge amount of instantaneous destruction rather than opening portals. when they inspect the controls for the skyship, have them in a fairly inconsequential location (IE anything that gets destroyed doesn't matter). If there's someone in the party that can be relied upon to push big red buttons, then give them a big red button that fires it.

Another option is to have the ship fold space behind it, collapsing anything that it moves through/over into nothingness. Have one button which, when pressed, glows faintly and the ship goes faster. Tell them "the ship feels like it's not even trying". Then have the ship go faster if they press it again. If they press it a third time, the ship jumps forward a mile, and everything on the line behind the ship is destroyed - mountains, buildings, whatever - all are destroyed by the passing of the ship. Then the jump drive has to recharge - make this pretty long to do, or make it need more crystals.

However, if there are constructs on the ship, are you planning on having it continue its autonomous mission to destroy Faerun? Do you want them to succeed? You could go any which way with this - have the party think they have control of the ship, then have a construct approach a control panel as they approach Faeron and have the doomsday weapon rise from the deck and start charging up. Cue the epic fight scene to disable the weapon before they get to Faerun. Perhaps have them destroy an outlying village on the way to emphasise its destruction. I don't know Faerun so this is going to be generic - pick perhaps 5 major targets in Faerun which, if destroyed, would classify Faerun as destroyed - districts or buildings or castles, whatever works. Then have the gun charge every 4 or 5 turns of combat and fire at one of these targets. If they can't stop it in 20-25 turns, Faerun is destroyed. Give them various ways to do this - kill all the constructs, destroy the ship, disable the cannons, re-program the constructs, remove the fuel cells - anything they decide to do that sounds like it would work. If they don't do anything, they will be seen as the destroyers of Faerun. If they don't get on the ship to stop it, they just have to hear about Faerun being destroyed.

The party could be seeking it on behalf of someone else, maybe hired by the insurance broker who insured the Skyships last trip, they either want the skyship claimed as salvage to offset the claim, or if it is reparable returned so they do not have to pay out the premium on the missing ship and cargo. maybe the whole thing is a scam, the skyhip was insured and then sabotaged by the party that insured it hoping it would be unrecoverable, the "cargo" is fiction, but they are concerned now the party will find that out and so want to stop them. 

This way the party have no claim on the skyship. If they try to keep it then they have a large organisation on their tail. 

An Airship is the fastest way to find out what they would rather do than follow the story.  Good luck... I hope it works out and they follow your plan, but I'm betting they are going to go other places first...

However, if there are constructs on the ship, are you planning on having it continue its autonomous mission to destroy Faerun?   

Yes this is what I plan on having the constructs do..... and I like the ideas you provided as well. I think having the constructs test the weapon and destroy a non descript mountain, to the surprise of the PCs. 

I have not worked out who sent the sky ship in the first place, to destroy Faerun. I am not sure if I will continue the adventure after this, but I may if I can come up with something.

Thank you for your suggestions. I will be using some of them.

I would limit the sky-ships "landing"/docking ability.

Aero-docking requiring special equipment.

Or so the original crash, might have been a failed emergency landing roll by a vehicle professional that crit failed.

Then checking the ships log would allow discovery of a list of Aero-docks.  ( Either scouted out ancient stuff if invaders or possibly built by the old ships crew.  Leaving the last construction Aero-dock outpost unknown by the sky-ship's command.)

Though I have a Spy Sky-ship "minor" more like real life keel boats that the government issue keel-boat in equipment.  Flown by a Raft-Cap'n that can land in rivers and float to a village, hamlet, or thorps river dock.

I have a possibility, consider the ship as a magic item that requires attunement of is heroic crew.

And with that attunement each member gains an invisible servant and a crew of tiny servants (number based on level of that crew member) that can't leave the boat/ship and the Ship a clock work side-kick (based on listed/attuned crew level) who also can't leve the ship without its spring winding down after a.. day, hour.. shrug.

I have what I call industrial circle magic, which you could use here.. the ship having it power formed by a magic circle that requires construction by several classes, specialists and individuals to succeeded.   And this circle is deliberately created, incomplete,  the last specialists or individuals needed are the officers of the crew.  With places for the living crew to put there names in the circle/log With a special stylus.