This was certainly the most difficult area for me having zilch experience in bodywork. I struggled with it initially trying to get gaps close and also the alignment around the windscreen. It is not perfect now but acceptable. I read the article in which kit from John Watson on fitting body and there were good tips in that.
The side panels need to be fitted first with a small gap between inner panel and dashboard, the dash can also be adjusted up if required. The problem is when you alter any one thing it affects everything else. To fit it through the roll bar I would allow a generous clearance, Marlin themselves do this if you have a good look, a tighter clearance would show up a small error much more than a larger clearance. Once the sides are fitted you can offer up the front and rear sections, as they locate on to the preformed joints they should be a good fit as long as the front of the panel is at the correct height, you can see this if you attempt to lift the panel up the gap will increase at the bottom of the joint and vice-versa. The front can be adjusted with shims under the hinges, the rear frame is allowed to move up or down on slotted holes. I also had to file out the slotted track to sit the back down further.
I hope this helps in some way, but everybody has there own way of doing things and this is just my way after a lot of head scratching.