sometimes I have to back up the doors with something because they are a little small.. usually I trim down the strut a little, glue it in the well, and then glue the door over that.. to both the strut and the edges. if the whells are menat to show a bit (spitfire and a few others) I glue the wheel and the modified strut in as well...
The only problem I have had is the Tamita Shiden (George), the wheel was exposed a little when it in the up position, but the wheel itself on the model was much too big to fit in the well... makes me wonder about the rest of the "scale" the model had... admittedly the real life plane had telescoping gear... but shrinking wheels??? I mean they were WAY oversized for the wheel wells...
But I stray from the subject, basically I usually do as you do... just shape the doors a bit and glue them in place... on most models it works.. and like I said, I have found gluing the strut in helps keep the doors in place..