Well, it sounds like; you are finding more, more leaks and those need to be resolved. For new parts, going to your VW dealers parts dept.; will probably, end up with id'ing the part of a greater evap related assembly (which is probably expensive; cost prohibitive; however, it maybe worth checking out), look at the online etka parts exploded views or revisit a junk yard, pick/pull for best prices and get what you need, confirming the parts are exactly the same (try to get the same part #'s; year of new beetle, etc.). New gas cap or seal; maybe, a good idea, as they are cheap and maybe contributing to these evap related issues, trouble codes being thrown and doesn't cost much to replace.
By the way, what smoke source; are you using, to do the smoke testing with? It would be great; to have access, to a real automotive smoke test machine; making leak diagnosis, so much easier! You are definitely, making progress; be sure to document things with photos, as this can really help, the next person with troubleshooting, similar issues! Thanks!
PS: did you replace the engine speed/crank sensor? (be sure to buy genuine Bosch sensors).