Definitely don't use Aircraft Stripper on Fibreglass unless you are extremely careful. As Charles already stated it will soften the top coat (gel coat) and will cause you lots more problems than if you just D/A or wet sand with a coarser grit.
I would recommend you D/A what you can without grooving or rounding out edges, then for a baby bottom smooth surface, follow up with maybe 180 or 220 Wet/Dry and wet sand it to eliminate that roughness you refer to, then prime using a Primer/Sealer (the Sealer is very important for fibreglass parts) with a medium to high fill factor. Give it a thick enough coat to allow you to wet sand to the countour and smoothness you want, then just paint as normal. You can also use Red Cap spot filler on any scratches, pits or roughness. You might give them a dusting of primer or sealer.
One note, I was taught, and I've not heard anyone say different, on fibreglass ALWAYS use Sealer. Fibreglass is known for leeching part of it's chemical composition for years, and if you don't seal it, you'll get a reaction to the paint you put on. Whether you use regular primer and then top it with non-sanding sealer or use a combination primer/sealer is up to you. I personally use regular high fill primer, wet sand to desired smoothness then top with non-sanding sealer that I give a light scuff to eliminate any nibs just prior to painting.