Sounds like you've got the difficult bit right already - the front and rear - so don't move them, at least not yet.
The bottom is usually simple - slacken the upright bracket that holds the sill rail (under seatbox edge) to the body (i.e. the bolts behind where seatbelt anchor points go) and you will be able to move that up/down/in/out as required. Might need to slacken some seat box bolts. (Having written this, I remembered mine has no actual sills, so it might not be quite that easy if you have sills.)
Top adjustment depends on what roof you have. With a hardtop (or, to a lesser extent, a truck cab) you can get a lot of movement just by slackening the bolts and the screen. Be aware that any stresses you increase or reduce on the screen frame could make minor differences to the bulkhead alignment.
If you are still a long way out on the door top, you can cheat by adding a washer or two under the galvanised capping, but it shouldn't be necessary to do so unless there's no other way. Hope that helps.