Not exactly about fitting the OEM exhaust, but I see there is also lot of exhaust competence in this forum. I recognize the challenges of assembly when I installed my OEM silencer. Keeping everything loose until it was fitted did the trick to me. I replaced Cobra 4-4 pipes with a perfect OEM silencer, no rust or dents at all. It followed the bike, and it looks new. The problem is a very annoying sound at certain RPM's. I am sure it is from vibrating heat shields, getting in contact at certain rpms. But I have not been sucessful in finding the exact location, and correct it. Any tips on how to proceed?
I want to raise a couple of things.
Yes to 'keeping things loose until it was fitted' so connections can be made properly. That's what I suggested earlier.
Next, please inform us about your riding impressions post Cobra 4-into-4 removal. Topics to be mentioned: throttle response, jetting changes (did you check for them, what did you find, if you did, and what were they changed-to?) seat-of-the-pants riding impressions, VBoost function pre/post-operation, and any other relevant material.
"Inquiring minds want to-know."
My experience is that the vanity collars at the points of attachment for the rear cylinders are not very-robust in their screws' dimensions, and I've not-attempted a re-fit of them.
About vibrating heat shields, all I could suggest is examining for contact where there shouldn't be-any, and perhaps a bit of cold-setting to gain clearances, or a bit of filing/grinding may-be indicated, if re-positioning of components doesn't achieve the non-interference/silence you seek.
The OEM headers are supposed to be double-walled, and in older bikes if the pipes have a broken/rusted weld holding them , one fix is putting an inconspicuous dent into them wherever the pipes seem to be resonating. It appears something like that may-not be your issue, as you have scored a 'in-good-shape' OEM system for installation (barring a manufacturing defect).
(88) Stock exhaust replacement | Yamaha Star V-Max VMAX Motorcycle Discussion Forum (vmaxforum.net)