I think you need to build it the way Z_Firebird wants it, since he is paying for it and all the work - right?
j/k
You're saving the car from the scrapyard - in more ways than one! Being a flood car, even if it were in great condition before, it's no longer in that condition, and will need a bunch of work to get it back. Your work, your money.
That being said, generally speaking, since there are many less first gen Firebirds than Camaros out there, and convertibles are more "rare" than coupes - there are some things to consider. But it's not a 400/4speed car, or a RA car, (or a TA), so you're in good shape to not "destroy" anything rare.
I'd suggest building it the way you want to - but also keep in mind your tastes might change as time goes on, and original cars seem to gather a little more "awe" from spectators.
Now for *my* firebird - a run of the mill 350 coupe, I wouldn't mind swapping the engine & trans out (but keeping the original), adding spoilers, painting it a different color, and adding different rims. These are all reversible modifications. When you get into cutting sheet metal, or dash parts, then I start to cringe a little.
As long as you don't tub it, gut it, install a full roll cage, and turn it into a pro-street dragster, I'm ok with it! (and if I wasn't - who the heck cares?! It's your money and your car!)
'68 Firebird, 350-4, 2 spd auto, triple black, Dlx Interior