It looks as though the motor has to drop quite a bit, the center line of the countershaft, the center line of the swingarm pivot and the rear axle at half the travel need to be aligned otherwise you have chain tension issues.I've built a few 500/250's like yours and always used the stock 99-02 250 airboot. I would not go with a uni type filter and a hose to the back of the carb, I know of people that have tried it and it did not work right. I have never used a 85 motor, but have used 86-88 version and the 89-04 versions, can't imagine the 85 is that much different on bottom case placement.