I haven't built this particular kit, but the instruction sheet is nearly identical to the directions for the 1/35 version Tamiya has been releasing since the '70s. I found that pre-painting things was the easiest way because some areas are a little tough to get at after assembly. The concerns about cement lifting paint isn't that big a concern if you take steps to make certain that the mating areas are left unpainted. Along the edges of the gas tank, for instance, you can just leave the edges free of paint so that once they are brought together, the plastic is left bare. Capillary action will pull the glue along the joint. If you're careful with the glue, it works well. Any problems can be touched up with a brush using thin layers of paint.
Tamiya's engineering is normally excellent and fit usually isn't a problem. If you wind up having to do a bit of putty work to disguise the joint, tape off the areas around the join to protect the work you've already done. Putty, sand, and adjust with the tape in place so that everything you have painted is protected, swapping out the tape when needed. Then, it's really a matter of touch up.