Instead of focusing the problems that could go wrong with this bike because of the flood damage there is another view that I think it is important. There is a very good chance that If I put some used parts on it to get it going again it could work out well and without investing too much money. This is a perfect excuse to put together a concours with ninja 1000 cams, carbs, and build a nice port and polished head and get the head milled as well. I was wondering though what are some good suspension upgrades. I was thinking about maybe putting some stiffer fork springs in ot to get it to handle better.
SERIOUSLY.. read your post... handle better? how does it handle right now?
you have a frozen bike, never rode it..
lets just dispell with the 'wetdreams',
Ninja carbs , and Ninja cams, and "ported and polished" and 'milled'heads ...(You have no clue to how to extract horsepower from this bike..) are not gonna get you anywheres.. youre gonna need pistons, rings, boring, ( did you even pull the head off, to see what's inside???) rod bearing, transmission parts, just to start... Ninja cams? man... simply put, the voices of us that have been thru this all, going nigh on 15 years, (on this 32 year old model...) when "we" began hotroddding the engine, can all say it's a pipe dream... ok? and SISF and I, along with others, actually had fully operational bikes as a start point.. making it simply a running bike will be enough of a challenge monetarily for you, and without it as an example of a "correct in every way" running Concours... well, I know I cannot disuade you, but man, don't be so bull headed. you have talked, and noted so many things you want to 'replace' with better, in these posts, and really have no idea of the probability of $$$$ you intend to dump, on a bike, that was locked up, rusted internally, bad harness, exhaust roached, and all of the invisible things we know, not just guess about, exist.
so the low mile bike, low mile chassis, low mile drive train, and wheels and everything right down to the steering head, and inside of the gas tank...and depending 'how deep it was sitting in water, and how long' are not really any 'deal' anymore.
best you rip things apart, and total up a simple "parts needed to make it a running Concours" very soon..
I'm really sorry, and I'm not just addressing "what could be wrong", I'm saying what IS wrong.. your view seems to be extremely 'optomi$tic", and in fact the only person being lead to believe any semblence of outcome, well. you decide.
I already noted spending $3k+ on a "totally customized nekid bike, sans fairings.. because I already owned a Conni.. my $500 parts bike made the big mistake of "starting" once I supplied fuel, and a battery... do I regret my venture... No. would I repeat it, or suggest someone else doing it... HELLNO.
oh, I'm the retired "tech Editor" for COG... so I know every part and it's price.
just tossin THAT OUT, again.
Carefully pull all the nice fairing and plastic parts off the bike...
contact Jettawreck, and sell them to him for the price you paid for the bike.. and toss the rest... you will be even then. I'm sure Jetta would actually give you $50 more, than you paid, just to get good plastic... as that all that I can say would be worth anything.