Hi Simon,
First thing to ask is, is the centre section in the correct position as per the manual (measurement from rear corner of chassis to corner leg on centre section, plus correct depth from side edge of leg to side of chassis) Orignally if the chassis and body were bought at the same time (together in the body chassis package) they would have been fixed down togeher with a set up jig that allowed us to drill and self tapper the centre section to the chassis in the correct position the manual has the measurements if not available I can send these on if you need them.
Once you are sure the centre is in the correct place you can set the doors if you are having difficulties two places where mods can be done to help, the large punched holes in the chassis that the door hindges mount from can be fettled to allow more adjustment incase doors or the body work have moved due to storage over time. The second place is if the filler neck decking surface is still free to move (As in not bonded down) you can push to a small degree this panel either backwards or forward as the case may be (checking with a windscreen as well) as you can either lower the top front edge of the centre section in relation to the door or lower it. This has to be done carefully I set up loads and it is fiddly but can be fun. We used to leave the centre section a fraction higher than the door as with time this could drop a mm or two but that was it. Do remember if setting the doors up with no components fitted (ie side perspex, mirrors, locks, door inner pocket, paint.... ) add the equiverlent weight inside the door as this was proved to create the best results.
As always hope this helps