How long was it after the wax/degreaser remover before you hit it with base? How about trying this next time.....NO wax/degreaser remover and just dry tack rag. Keep the first coat of base as a drier coat to start since that seems to be helping.....

parts look real good the one part has contamination silicone or something. you did the right thing by misting over the contaminated spots. any time you get a random fish eye you can usually cure it be letting it flash to the dull stage. then apply a light fog or mist or dry coat what ever you want to call it. letting it also flash dull you may need to do this 2-3 times then you should be able to continue with normal coatings. on your micro bubbles your not still heating your paint materials are you? you might try and apply it just a bit lighter. you my be putting it on to heavy, base doesn't like to be applied heavy like other paints , urethanes, enamels. 2-3 light med coats rather than 1-2 heavy wet coats.
Jay D.

Thanks for your tips.

Yes, I'll try not using wax/grease remover.
I normally wipe it on then mix my paint. But I would imagine once its evaporated and you cant see any wet areas it would be ready to spray? Is that not the case?

microfiber towels arent good to use with WAG.they led me to quite a few headaches. i dont even use them brand new when detailing- they always go through the wash first.

I not sure on the WG remover. Friends of mine in the chemical industry tell me there is more and more pressure on them to recycle solvents. I think we are getting some minor trace amounts of contamination right in some of these prep. products. Possibly even some very slow flash off stuff. I find myself using less and less of solvent style prep.s and doing more sand/dry rag/ tack rag...... I can't even remember the last time I had a problem with base coats.......hmmmmmmm....... I don' use micro fiber rags for anything but detailing so I can't really comment on those.....

Well thanks for all your input guys.
I've finally finished the project.
Clear went on great. Bought a Mirka Shark blade to cut down all the nibs. Then wet sanded with 3M 3000 grit on the DA, and polished with a mini air polisher and 3M fast cut, and finished with 3M Ultrafina, then a coat of Farecla Wax. Came out fantastic. Best I've ever done. Going to start now on my 1999 BMW 540i front bumper next, I'll post the progress and see if I can eliminate some of the issues I had with the base coat on this project.
Pics...

looks awesome, and yes let us know how the bumper project works out.
Jay D.