Super common issue as others have said. My experience was to soak the hell out of the nuts and studs with PB BLaster for a bunch of days, and it allowed me to unbolt the door tops and then soak the studs for a couple more days to got them out without worry. I ordered a stainless set from either Atlantic British or RN- and also the seal that goes between the door top and bottom. I couldn't believe how much thicker the new seal was compared to what possibly could have been original from MOD. As others suggested, a new seal will realign things much better. I did actually do some slight bending which helped.
Another suggestion is if the seal doesnt come with adhesive, you will want to stick the seal to the window/top section of the door- that way, if you run with the doors half off, you wont have weird weatherstripping flopping around.