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I picked up a very clean 85 a couple of months ago. It had no spark so i found it to be a bad cdi. When i replaced it i had spark lights etc. After the first run i ended up melting the pto side piston. I had a good motor out of my 86 that i had that ate a seawall. Got her running again. Now after changing my mains and power jets to fatten it up for todays lovely gas i have a bad bog at mid range. Almost sounds like it cuts one cylinder out. Whoever had it before me disconnected the t.o.r.s. and the ignition control unit is out of it. would that have anything to do with my bog? If i start at a dead stop and go wot it seems fine. Any help would be greatly appreciated. Also the frame vin is an 80n..And the engine that is in it that came with it is an 8x. Not sure if that meens anything...just curious.

If your sure the carbs a completely clean, including all the passages I would look at the moving the needle up or down depending where it is now. The mid range is controled by the needle and needle jet. Often just changing the main won;t have much effect in the mid range because when the carb is only have open the needle is the restriction.
Not quite sure what you mean by "the ign control unit is out of it"

The needle is set to the richest setting possible. Position 5 i believe. I did notice that my fuel pump vacume line came undone. I replace both of them but it still seems that it has a backfire in the low end. I have not ridden it to see how the mid range is now with new vacume lines due to the fact my pto side exhaust flair on the pipe broke off. I have the low end air screw out about 3/4 on the pto side and 1 turn out on the mag. The ignition control i am talking about is a small grey box with three wires coming out of it mounted to the airbox. Thank you for the response..I just wish these were not so hard to tune. I did not have this many issues with the 86...just braking a brake cable at 70mph and hitting a sea wall.