Before we start, what are you current jet settings? Was or is the bike currently running fine with the current jets? If not, then with no air box lid and an FMF system you will have to go rich on the jetting as the extra air from no lid and the FMF both lean the air/fuel mixture. You might even have to go with a richer needle too if the 4th clip position is not enough. The elevation only matters if you are above 5k feet. What you will have to factor is temperature. Colder temps need richer jetting and vice versa.
As far as not knowing if you have an 85 or 86 model, check the VIN for the 10th digit. 85 will be "F" and 86 will be "G."
Suggestions:
1. As you said, buy genuine Mikuni jets. I get mine from
www.JetsRUs.com2. Adjust your float arm according to the manual. This should stop it from overflowing the bowl and coming out the overflow.