That is a sticky one David (no pun intended). With the self adhesive I would tend to fit in before painting the side walls even though the RLM79 would not match. Reason is that I do not know how well the self adhesive would work over a paint surface, as with glue on paint there is a likelihood that things will come unstuck. If it was just a 1/48 scale I would not be over worried about the paint mismatch as little will be noticed once the cockpit is sealed up, but I cannot comment on a 1/32 scale. Even so in your scale I would tend to try and match the paintwork while the PE is still on the adhesive backing sheet by painting the PE with a very fine brush and very little paint on the brush, a slow, tedious and delicate process. When dry and sealed, then place onto the side wall and paint round it, again, slow and easy and if spraying, mask well.