These are some of the things my bike needed when I got it. They're pretty typical for any '91 - '98 carb'd 900ss.
Air box lid - quite often they've been cut up or deleted, with a small frame used to hold the air filter in place. My bike had a K&N filter with a metal frame. Some people say this buys you more power. It probably does if you jet for it. I don't care, I think these bikes are too loud with no airbox lid, so I found a stock one and reinstalled it. I did remove the intake snorkels though.
Carb Rebuild - I used a "Factory" brand jet kit and followed their recommendations for baseline settings. Time will tell how close this is. I also bought new emulsion tubes - the bike had been fouling plugs and these tubes are known to wear. The wear on the original parts was pretty obvious when I pulled the carbs apart. With a season of riding on the 900, I haven't had any issues with fouling plugs and the power delivery is smoother.
Droopy mirrors - fixed by pulling the mirrors apart and roughing up the joints with emery cloth. I hear this isn't a permanent fix but it's working so far. Or it was... I had to do the right side miror again this summer.
Leaking clutch slave - I bought an Evoluzione piston for the stock cylinder, along with a new rubber bellows (from the dealer). It's more popular to replace the entire cylinder with an aftermarket unit, but this is cheaper and works fine. Aftermarket slaves can provide a lighter clutch pull. I never thought the stock lever was bad so didn't think I needed anything different.
Battery cables - A common mod is to install heavier battery cables. Be careful when discconecting the starter lead, it's not uncommon to spin the lead in the starter motor and have to replace the brushes. Ask me how I know. This leads to...
Rebuilt starter - the terminal corrodes and the insulator breaks when trying to remove it. Replacement brush kits are available but they don't come with new insulators so you have to improvise. This is also a good time to check the bearing and bushing in there too.
Gearing/Chain - A popular mod is to go up to a 41 tooth rear sprocket. The countershaft sprocket was worn on mine so it was a no brainer to change everything, going with the more popular 15/41 gearing. When checking these parts on a new to you bike, also check the sprocket retaining plate.
CS Sprocket retaining plate - these DO wear out. I discovered mine was over 50% gone and overdue for replacement. Once they wear out, the sprocket can move around and bad things can happen. They're cheap, replace them with the front sprocket if they show any wear.
Clutch cover - not ususally a problem, but mine was damaged. The SPs came with carbon fiber covers. This one had been damaged by overtightening the bolts. Plus, when the clutch plates were replaced it looks like the pressure plate wasn't indexed correctly and didn't seat all the way. When the bike was started, the retaining bolts rubbed against the cover and discolored it. No biggie, I'm not a big fan of carbon fiber anyway. I got an aluminum aftermarket cover which is open but should still offer more crash protection than the stock unit. I wanted to get an older style stock cover but got impatient and bought the aftermarket part instead. Now I need to get stainless springs and caps to put in there so they don't rust.
Seat - I hated the seat on the '97 so I bought a Sargent seat off eBay. The first time I rode the bike I wasn't sure the new seat was much of an improvement, but the more I ride the bike the more comfortable this seat feels.
Windscreen - The stock one was scratched and rubbing on the temp gauge (which happens when you install a screen for an older SS on a newer bike with a temp gauge) plus it had two holes drilled in it to mount what I'm assuming was a radar detector. I didn't HAVE to replace it, but did anyway. The new one is tinted, not sure how I'm going to like that but thought I'd try it. (And at the time I was seriously considering painting the bike black)
Battery - AGM It took a while to find one but I did. Try dvoltbatteries.com. So far (fall 2009) it's worked great. Combined with the new cables, I have zero starting issues. Push the button and the engine WILL turn over, no hesitation or doubt.
Battery straps - These bikes are getting old and the straps have deteriorated with age. These are still available, if you're pulling the airbox to rejet anyway, replace these too.
New Belts - Good insurance for any new/used bike. In my case, the old belts were so loose I pulled one off without even loosening the tensioner. Yikes!
Valve Adiust - when I checked the valves, only one of them was out of tolerance but a couple more were very near the limit so I ended up replacing three shims.
Turn signals - the rear signals on this bike had been replaced with flush mount, carbon fiber-look lights. I bought stock signals to replace them and luckily got a new rear fender in the deal too, as I found the old fender had been modified to use with the aftermarket signals.
Suspension rebuild - I had to remove the rear shock to adjust the valves. While it was off I decided to have it rebuilt/resprung to my weight. And as long as I was driving over to the suspension shop (Department of Suspension) anyway, I pulled the forks too for the same treatment. I've never had a bike with the suspension set up for me specifically. The rebuild ended up getting more involved than originally planned, with the stock internals being replaced with parts from a Superbike fork. I FINALLY got to ride the bike on some twisty roads with the new suspension - on a recent trip I got off my stock 996 and climbed on to the modded 900ss. For "enthusiastic" riding I prefer the 996, but looking solely at how the suspension worked, the 900ss was better. Now I have to budget for a suspension rebuild on the 996!