tips for spraying primer

Matthew, I'm not sure how much of what you're seeing is solvent pop. When you use a roller on something like a 4:1, you're laying on a LOT of material. The nature of a roller would produce air bubbles if you rolling a little too fast, and the thicker the material, the higher propensity for bubbling. If you've sanded most of the high build off, then I don't think you should encounter too many problems.
Dcg333 has a very valid point with the trapped solvents, which is what I explained in one of my original replies. If this was paint, either base, SS, or clear, I'd give you the same advice, sand it all off and start over. The fact that it's urethane primer, that has been mostly sanded off, and has had ample time to off-gas, I would just carry on as you plan.
If you get the 2041 reducer for your 4:1 urethane primer here's what I would do. Mix up enough properly reduced and thinned material to fill your spray gun cup once, and spray the hood and trunk lid. You may get one coat on each or you may get two, but from experience, I'd say you should get one good coat on each panel. Let this dry completely for a day or two, especially if the temps are below about 15C. Then, take your long board, some 180 grit dry sandpaper, and sand GENTLY. In other words, let the sandpaper do the work, don't be pushing on the board to try and get a faster cut. :) During this process, watch for ANY sign of the original craters from your previous primer coats. You know what they look like now, and you'll kow if they get any better or worse after this thinned primer coat. If it looks like the primer is doing the job, do the same with the remainder of the car. If it looks like the original craters are still there - STOP - and go back to where you originally started prior to rolling on the first coar of urethane primer.

Also, the P-sheet for your 4:1 primer calls for a 15 minute recoat window, and a 10 minute recoat window if you use the 2041 thinner @ 10% of mixed product. CAUTION: These times are for ambient temps of about 19C, so, with temps in the 12 - 14C range right now, I'd double those time to be on the safe side. You don't want to trap any more solvents now, do you? :)

Hope this helps, and good luck.