While I can appreciate the money/work/time you've put into the bike, I really doubt you'll get $3500 for it. While to a "trained eye" the bike is something special, to the average Joe Shopper it's just a 22 year old bike with a few extras. Not many people are going to put down over 3 grand for a 20+ year old bike, regardless of it's horsepower. Plus the Stage 7 kind of hurts it's "driveability", so again, to the "untrained" person they might think it's not running well.
Case in point: It took me nearly A YEAR to sell my '85 Magna V30. Bone stock, but it virtually mint condition, not a single thing wrong with it. I was asking $1250, and kept getting low-ballers offering me a grand or less. I was in no rush to sell it, and held out. Finally this spring a guy came through and put my asking price in my hand. While I realize a 500cc Magna isn't half the bike of a modded up Max, it's the same idea. You can find bikes much newer for a lot less than your asking price, so unless someone is looking specifically for a Max I don't think you'll get any serious offers for your asking price.
Like EvilD said, money into a vehicle does not equal money out. Buyers see aftermarket goodies as a nice bonus, but not something they're willing to spend extra for. When I was looking for my Vmax(I had my mind set on a Vmax at that point), I was in a toss-up between two bikes. I found one on craigslist locally for $4200, it had like 20k miles on it, a '95. Bone stock but overall good condition. Found another on eBay in Vermont for $4900, with all the extras...stage 1, holeshot slipons, aftermarket blinkers/taillight, frame braces, fork brace, R1 brakes, chromed scoops, shift light. It was a '97 with about 14k miles and in MINT condition. In that case, the newer year, less mileage, and extras convinced me to cough up another $700. If the year and mileage had been the same though, I doubt I would have gone for the bike I did. While all the accessories added to my bike are easily worth a grand, somehow as a buyer I didn't see it that way. More like I was kind of leaning toward the newer bike, and it coming with all the extras just sealed the deal.
And while KBB/NADA book values are nebulous at best, buyers often take them as holy gospel to what something's worth. You're selling an '88 Vmax, not a rocketship on wheels that'll smoke almost anything on the road. For $3500 that's a performance bargain, but that's not what the buyer sees. They see a 20 year old bike in nice shape, and KBB says it's worth $2800, so that's the absolute max they're willing to pay.
You could pull all the goodies and put it back to stock, but that's a lot of work and you're not going to get anywhere near what you spent on them back out anyway. It's your call, but I'd sell it as it.
If you're in a hurry to sell, I think you're going to have to reduce the price, or be willing to dicker a little bit. If not, just bide your time. Somebody who knows what they're looking for will come along and realize what you have isn't just a 20 year old bike.