Lets not get ahead of the game here. A BB turbo is nice and all, but not needed at this stage of the game. Let's get the car straightened out first. Don't know why your 60' dropped off with the taller tire. My GN seemed to like either. 1.58 60' on a 26" DR to a 1.57 60' on a 28" DR. It did go a 1.54 60' on a full 28" MT slick though, but thats besides the point.
1st question: When you race, are you letting the car hit OD or are you running it in 3rd for the full quarter mile? Letting it hit OD will bog the car and lock the convertor. Load on the engine decreases ( i believe) and boost will drop. Not to mention heat up the trans. You can lock it at the line via a switch or use the old school paperclip method in the ALDL port which will force lock at second gear upshift. Cant remember what pins though.
2nd: are you running the wastegate "tuner" style? Basically this eliminates the factory wastegate solenoid (most modern chips dont use them anyway) by running a vacuum line from the turbo scroll straight to the wastegate actuator. Do you have a RJC boost controller?
As far as valvesprings go, if the engine has any miles on it; I'd replace them. Comp 980s work well and I've had them in both of my TRs with stock motors. No problems. Some people like the Kirban "LT1" valvesprings, which is basically a stock spring off a Chevy LT-1 V8. Some say they have too much seat pressure at 100lbs. I have no experience with them. The Comp 980s install fine right out of the box, and I did not reuse the stock cups. Some say you can, I chose not to. No issues with that. Grab some new intake valve seals, plugs, and valve cover gaskets and you're good to go.
