Will a transmission from a 5.2 bolt to a 3.9 engine?

yes.

manual bell housing and auto trans.

3.9/5.2 use the same flywheel or torque converter

a 360 will need a external balance flywheel or torque converter but use the same auto trans or manual bellhousing as a 3.9/5.2

Magnum engines (3.9, 5.2, 5.9) use the same transmission bell pattern as LA small blocks.

And so does the 4.7 and the 5.7 from what I've read on the Internet.

3.9s and 5.2s are internal/neutral balance, 5.9s are external balance... But not the same balance as an LA360 that's external balance. So you are using a carb, any internal balance LA flywheel/converter will work as well, as long as it works with the trans as well.

But, if EFI, you can't use a 3.9 flywheel/converter on the 5.2, and vise versa, because the 3.9 is only a 6-cylinder... The tone ring only has 6 windows/notches for the CPS. Obviously the 5.2 needs 8 windows

It'd be like trying to run a V8 with a 6-cylinder distributor.