86, 87, and 88 had same KIPS setup, 89 -04 is different.
There are marks on the drums and shaft, although they may be worn off. In the idle position the the shaft should be into the cylinder, and when revved the shaft extends out of the cylinder. This doesn't mean they are in time, if you remove the exhaust pipelook into the exhaust port the sub ports should be closed withe the KIPS drums, if you pull the rod out the drums will rotate and open the sub ports, if they are not that could be your problem. Also the carb was a Mikuni, it worked OK but not as good as the Kehin, anyway it would be my guess that the jetting is off or the KIPS is not funtioning correctly. What do base the jetting be on from, the bike runs like crap so how can you be sure the jetting is on?