Howdy Paul, I'll drop my two cents into your bucket...
I agree with GMorrison, try to knock out this task first. I know it may not be possible, but the earlier you do it in the build, the better.
For what it's worth, I've only built 3 kits in flight, but I've used two processes for closing gear doors both permanently and temporarily for painting.
For larger wells, like my 1/32 Revell Corsair and my 1/72 Space Shuttle, I stuffed the gear bays with wet tissue or paper towel first. Then I used the gear door to "smash" the stuff down until the gear door is flush with the surrounding surface(s). This gives you some backing so that the gear doors don't fall in during glueing. Also, it give some rigidity to the area for any subsequent filling, sanding, and rescribing.
Unfortunately, you can see I accidentally scribed through the seam on my Space Shuttle. I didn't notice this until after I painted. Since this is just a ceiling hanger for my classroom, I didn't bother to fix it. You can see the Corsair's doors came out much better.
So, the second way I've attached doors is by using Silly Putty instead of tissue. I used a bit of Silly Putty on a 1/48 Sabre because the bays were much smaller and I only needed a little ball. A negative about SP is that it doesn't offer the rigidity that the dried paper towels do. Also, I don't know if there'll be any long term chemical reactions between the SP and styrene.
As an aside, the SP method is a great way to temporarily tack gear doors in place while painting the airframe. The paper towel method works too if you tack the gear doors in place with white glue.
Anyway, I hope that helps a bit. It's a drag that gear doors don't fit as well in the closed position as they should. I think I'd be more inclined to build more in-flight models if I didn't have to deal with the doors.
Good luck with your project(s)!
Cheers,
-O