I used a TwistedPins custom stencil for the Star Trek: Mirror Universe cabinet.

I would only recommend their stencils for a complete repaint of a cabinet.

1) The stencil will lift paint if it's even marginal. I had their stencil lift toner off of a water slide decal... so loose paint = no.no.
2) Their stencils are single use only. Get it right the first time; no chance to reuse the stencil later as the material self-distructs when you remove it.

I traced my artwork and sent it to them... after getting it ready in my computer.

PERSONALLY; I'd use some blue painters tape and a xacto blade and mask off the colored areas and just reapply the black paint.
The art looks to be in pretty good shape.

Getting the side rails off... I'm assuming they are similar to the Bally's of this era.
I did mind my pushing a plastic drywall putty knife between the wood and the rail at the screws. Then using a prying movement loosen the nail enough so you can get pliers and/or a hammer claw under it. Then pull the screw out.

Once you'r ready to replace the side rail; you can buy the nails themselves from PinballLife
or PBR or even Mcmaster-Carr.com. I'm trying some new nails from McmasterCarr on my MirrorUniverse; so we'll see how they work.
Anyway; PBR has them as:
Siderail Nails (#GTB-FA-701) $0.18