If I'm reading correctly your other cab only has floor rust & corner rust...correct? If it's a good shop or welder/fabricator who knows how to do chop tops or sections like that, then I'd trust them either way. If you're going the custom route and want a chop top, obviously now is the perfect time lol
If you question the shop or don't want any chance of mis-alignment, then just fix the cab corners/floor on the other cab and call it a day. Then there's no cutting of the top portion of the cab and no chance of mis-aligning the two pieces and having your doors or windows out of wack. Of course it'd depend on how the two are spliced together but if they are off at all, then the geometry is out and usually noticable.
Either way, with a good fabricator anything is possible and should work fine. It's usually not worth the cost to try and repair the window channels and the fabricator better be very good and have a lot of time on his hands. Although it'll most likely still cost more to repair the channels than to splice the two cabs together.
