I think youre problem is water in the electric components around the plug/coil area. Clean connections, use dielectric grease, and perhaps electricians tape around the coil"wire" down to the plug, to make sure the connections to the plugcap is waterproof. Also make sure that the plugcap is sealing against the plug, so water cant enter.
As for the 2 fueltaps, its so you can get every drop out of the bike, so you dont have a couple of liters fuel in one of the wings which you cant use. But yes, you can just hook up one of them if you want to.
As for top speed. Youre bike is generating the maximum amount of torque around 5500rpm as i recall, so at 4000rpm, it just cant accelerate with the "heavy" gearing. Mine (2003 xt600e) runs 4000rpm at 100km/h with stock gearing 15-45, that should be better for you. So try to change gearing, im sure it will help. Mine runs about 130km/h-ish flat out, it was faster once, but thats many kilometers ago =)
I usually dont exceed 100km/h anyway, so its okay for me. Usually im cruising around at 80-90km/h. I dont like the interstate too much, but go there from time to time when I have to. But theese bikes shine on the secondary roads
Hope this helps.
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