I forgot the pregen had 16's, I don't know what options are even available for that, if you do go up to the 17 you'll have a lot more choice. I have sometimes run shinko's (can't tell you the model off the top of my head) when i'm looking to save money, I can get get right out to the sidewall pretty much on warm dry pavement, but I don't like the feel from them. my preferred tire is the Bridgestone battlaxe BT-45, it's a dual compound with pretty good characteristics all around. I go through 3-4 sets a year so i've been experimenting lately but it's still my favourite all around for our bikes.
As for forks, to my knowledge, the pregen forks are 36mm, the new gen 250, and the 500, are both 37mm. switching to a new fork diameter is often a pain. I'm not sure if you can get away with 1mm by using a shim or something, someone else will have to answer that. But if you're going through the whole process of changing out tripples, you'd be better to go with a modern fork with all the adjustments. Otherwise, i'd suggest just doing a good setup on the forks you have, changing springs, spacers, oil weight and amount, ETC, will allow you to get the proper sag and damping for you and your bike, it just won't be adjustable. You've seriously modified the bike and it's weight distrubution, the forks should be readjusted to compensate. @
DannoXYZ might be the best bet on this one, since he races I assume he has his suspension dialed in.