First, yes I would suggest using a primer anytime you're going to paint over bare metal. The primer gives the paint a clean surface to stick to. I too used high-temperature stove paint, but others use engine paint sold in auto parts stores, and it appears that it works very well.
I can't help you with the lid. I used a Weber lid, and I understand that's not an option for you.
The 12" thermometer that you describe sounds like the right one to me. The thermometer is removed to allow you to take the charcoal basket out. Then it's installed after the basket of lit charcoal is put into the smoker.
It sounds like you're moving right along, and you're almost there. Good luck!
OTS - UDS - Don't have a UDS? Well why not?