Oohh that’s a problem, is the frame paint or powder coat, because I recon some frame remedy will be needed.
My S/F frame was pretty bad (see 53 Superflash resto) it may well have been cartwheeled at speed into an vintage locomotive at good steam.
So always do a dry build of everything.
I practiced fitting the empty engine/gearbox and left generator mount quite a few times prior to any painting, also fitted everything and only then had an exhaust system built, as the left down pipe has to literally thread a needle.
In short not an easy Bike to build by any stretch of the imagination.
Best of luck, and if you want you are welcome to see mine for a visual check of fit up.
Thomas