Pinholes: Usually not a problem unless fairly large and/or shining on the paper, but best to fix. Google "pinhole in bellows repair" and you'll get some options. Easier in an enlarger (vs. camera) as the bellows typically aren't fully compressed. I'm willing to bet that 3 out of 4 Beseler 45s in use now have pinholes if you check carefully.
Motor: Cracks in wiring insulation should be repaired. Motor smell may be dust, bearings, or just the belt. BTW, I believe every outlet in a darkroom should be on a GFCI.
Replacing parts is one thing, but restoring as you described will be a labor of love. Great if you have the time to do it. But, if it's that dusty, you need to clean it anyway so maybe that puts you halfway there.
I can provide many used parts, but I'll be out of town a lot over the next few weeks. Parts list for the most recent versions
here.