The Rustoleum plastic primer/adhesion promoter is fantastic stuff. After using it I can actually mask the painted handrails to paint the ends white. I can't even look at un-treated handrails without flaking the paint off.
As for together or separate, I always prime and paint my handrails separately. Despite saying 'primer' on the can, the Rustoleum plastic primer is technically a mix of solvents that slightly soften the surface of the plastic so that the subsequent paint will form a strong mechanical bond. This is what makes it so good for Delrin handrails (and why they tell you to spray the paint coat within 10 minutes of the adhesion promoter), but also means I'm hesitant to use it on the much less solvent-resistant styrene shell of the loco.
On the less-effort flip side, since the adhesion promoter is basically pure solvent you can spray it on right out of the can (make sure you have good ventilation!) and any excess will evaporate off the part rather than forming a big ugly paint blob.
Finally, as for the handrail holes, I've never worried too much about them. Unless you're applying the paint with a popsicle stick very little of it will make it inside the holes in the shell. If a hole does become so clogged up that the handrail won't fit back in I'll start with a #80 drill and work my way up one at a time until I find the bit that's just large enough to ream it out. But out of hundreds of handrail pegs I've had to do that maybe twice.
