Yesterday I got my real Conti GT back. It's running well again.
Covers, seat and tank were off. I noticed the hose clamp on the fuel line at the injector was loose. That may have been a problem. My fueling was awful. Idle was hit and miss, mostly around 1000 rpm. It would be idling, then poof. It was like the plug was pulled, stopped. The fueling would surge and buck, and cut out.
I put the PCV box in the tool bag box and ran all the wiring up from there. I got everything snapped together. I organized the maze of routings, injector cables, fuel line, all of it. Put in a zip tie here and there. There is no rat nest visible.
The stock header is gone, replaced by the Carpy header I bought months ago. The angled Sportster muffler has been melting boot bottoms and my synthetic cloth cuffs of my pants. I added some exhaust wrap around it, using the stuff that came with the bike when I bought it. The Carpy header has no lower bracket for attachment to the frame lower. After the whole exhaust was bolted in, I wrapped a hose clamp around the pipe and the frame tube to replace the added stability of the lower bracket. I finished it off with one of those chrome covers from CMW to cover the plumbing at the header/muffler joint.
I adjusted the idle up. Thanks, Arizoni, for posting that anti-clockwise raises the idle speed! I kicked it over, starting on the second kick. Raised the idle again. Took off for a test ride. Excellent fueling and idling at 1200 rpm. The motorcycle I bought is back, thumping like a clock. I feel much better now.