Omegaprime02

As far as actual game advice, I'd recommend against doing that, at least for now.  Actually I'd suggest just building a normal character, and then throwing in a power or two to reflect the fact that you've got this ship somewhere offscreen.  For instance you could have an "artillery barrage" power that is just a big area effect attack, with a limitation that it takes an extra phase or two to use, and you have to be kinda close to the "ship" to use it.
 
12D6 Energy Blast, Explosion, lands at end of next phase (-1/2 maybe), must be within 10 miles of a body of water (-1/2 maybe, presumably the ship is always nearby somehow).  No need for a really complex build, it's just presumed that there's a ship out there somewhere.
 
You mention you want the character so that it's revealed at the end of the campaign that it's really the ship that is the character.  That's easy enough to do without going into a complex character construction.  Basically you talk it over with your GM, and decide that for the last X number of game sessions, your character will change and you'll swap out to a vehicle that you built for that occasion.
 
Think of it like the recent Captain Marvel movie.  Mild spoiler alert if you haven't seen it:  In the last 5 minutes of the movie the character gets a huge power up over what she had throughout the first 95% of the film.  Effectively she spends the whole movie at one power level, and then at the end she gets her big finale where the GM hands her a new character sheet that is waaay more powerful.
 
If you just want the power increase at the very end, there's no reason to build it into the character you'll be using for most of the game.  You can just treat it as a story arc for your character that concludes when the game wraps up.  Now, if you want that big powerful guy for most of the game, that's different.  You probably need to find a way to build that.  But the longer you are clearly head and shoulders more powerful than the other characters, the more their players may begin to resent it.

One last point -- you don't have to construct every aspect of the character, particularly if it's really unusual.
 
Suppose I wanted to play a hero that is the psychic projection of a little boy in a coma.  The kid's dream manifests itself as Captain Amazing, superhero.  This can just be a background description for my character.  I don't have to create the character sheet of the little boy.  I don't have to worry about what powers the little boy might have, or how it was purchased.  I just declare it to be so.  I build a regular superhero and then note it on the character sheet (or even just keep it in my head if I don't want to reveal it to anyone) that somewhere out there is a kid in a hospital who has created Captain Amazing.  But as long as it stays a background element, there's no need to try and model it with game mechanics.

So, just a quick mention that I don't think other people have covered.
 
One problem that you will run into is that when you build something fairly non-traditional like this, there are going to be like 50 different ways to do it.  At least one of those ways will be ultra-expensive, and at least one of them will be ultra-efficient.  Seriously if you experiment enough with it, you'll find a character build that is super-powerful compared to everyone else's character.  It'll be perfectly book legal, and it'll be crushingly powerful.
 
Now, that's only a problem if it makes people in your group upset.  If everybody sort of agrees that it's your turn to be the ass-kicker, and they all have a good time with it, then who cares? 

You know, the idea of what is the base character is meaningless in terms of gameplay - in either case you are going to have two entities, one with the party and one remotely.  It is the mechanics that change.  I like Massey's version of the character, I think this would be easy to play in a face to face game because everything is going to make reasonable sense.  If you build it the other way there are likely going to be little things that do not quite work the way you think they should and require tweaks and changes until they do work.
 
As far as the clairaudience thing is concerned - to get around the need for the physical manifestation to interact with things in a game mechanical way, I think I would also buy a summon Avatar style power and make that avatar the physical manifestation of the clairaudience.  That means that you would have a thing that can walk talk etc etc without any handwavium involved by allows the ship to target stuff nearby and be completely informed of what is going on.  It would also mean that when the avatar is wasted by some attack, you might still be able to attack as the visual component of the avatar may still be active, even if the avatar itself is dead/broken/smashed to pieces... (I have a picture of half a face lying on the battlefield with the eye tracking the bad guy and a salvo on its way...
 
Doc

So this idea interested me so I took a stab at creating it how I would do it. I obviously don't know your campaign limits, house rules, etc... So this was just an attempt to cover most things and keep it close to 300 points. Very hard to do! His skills are very weak, plus there is other stuff I am sure he should have, but without reducing his characteristics even lower or cutting powers he would/should have this wasn't possible. I didn't spend time on complications or so other details (didn't build out the ship which is a floating base in this build). 
 
Anyway, I've attached here. 
Ship Avatar Character.pdf