I took my 78 F exhaust off every year to repaint it. My chrome was a mess so repainting them was the easy fix.
I guess i don't really understand your problem, i always did it by myself.
I installed the complete header in one step.
I used masking tape on the header pipes to protect my new paint. And also to hold the 4 clamp rings ( i don't know the proper name) in position. These rings need to be held not where there will end up once installed but down the pipe a couple inches, just before the bend down. So lots of masking tape is required. Don't skimp here or the clamp rings will slide down the pipe and you may have to swear at it.
A large block of wood under the bike for the pipes to rest on.
Put the header pipe in place.
Get 2 sleeves in place on one pipe, free the clamp ring from the masking tape. Push the clamp ring into place over the sleeves. Put the nuts on LOOSELY.
Repeat for the other 3 pipes.
Or maybe i am just not understanding your situation, that happens to me more often then i would like.