Yeah, I used a heat gun + scraper to strip the finish of my Jaguar Bass and it is a pain in the ass. The body has a lot of contours and they can be tricky when using a scraper. I was very cautious with the gun so mine took longer than it should have, I think, and in some areas I ended up with little spots of the finish still intact. I used 80-grit sandpaper to get rid of these.
Supposedly if you are skilled you can get rid of the poly and sealer underneath all while using the gun/scraper technique, but as for myself I spent weeks sanding the sealer -- that stuff is bombproof. In total, because I was being overly cautious as it was my first time, I probably used 30 hours ridding the body of the fucking sealer. The sides were terrible. I found that there was a lot more on the back than the front. Do not be afraid to use rough sandpaper to get the majority of it off, move up to a finer grit and it'll clean up just fine. If you're using something like 320 on the sealer you may as well be rubbing it with a dry cloth. I definitely have to +1 the dust mask, get a real respirator mask (like $20) because you're going to need it when spraying anyway. I almost have a fondness for the oddly sweet, most likely harmful smell of warm sealer now...
Anyway, the main thing is that you really need to get the body in great shape, even more so when it's not gonna be a solid color. It sucks and at times you might lose the drive, but if you cut the preparation process short you will hate yourself if something goes wrong. Sanding is the WORST. I'm pretty sure they make you sand things in North Korean death camps. I thought I would spray an alcohol-based dye on after sealing it, so I hit it with a thick coat of sealer and then discovered that I have zero confidence in my ability with a sprayer. So now I'm sanding away sealer ALL OVER AGAIN YAYYYY
Currently I'm about to use Transtint water-based dye to stain mine, I didn't know there was stain with poly in it...that sounds like a real help.
Check out reranch.com if you haven't already. Their forum members are super helpful. I got a 3-page PM from this guy giving me tips on the entire process.
edit: The process has taken my lazy self TEN MONTHS. I had a few setbacks and at one point I was fucking done and put the sanded body, parts and some accessories up for sale. Luckily nobody bought it because I would have instantly and forever regretted that. I have, however, learned a lot in this ordeal.
It just struck me that you might have done all this before.