Sorry you are having some problems with your New Beetle;
unfortunately, we have all been there! 
Sounds like most, if not all of that work needed to be done! However, seeing how you're spending so much money on this car by having repairs done by a professional technician; there are some ways to help with high maintenance costs,
by starting to fix things yourself. Due to the nature of these modern cars; you really need to get VW compatible scanner, to diagnose and figure out what is going on, when the check engine light is illuminated. There are some pretty inexpensive ones out there; $40 on the low end for the basic code reader Autel VAG 405 or $250 for the high end professional scanner, (that works with a windows based PC) called VCDS, from Ross Tech. I would go ahead and order the basic code reader scanner (VAG 405);
meanwhile, go ahead and get your car scanned at your local auto parts store, for free. Once you get the codes from the scan; then go ahead and post the codes up here. Then, we will see if we can help you figure out what the problem might be and you can attempt the repair with our help!

Just buying replacement parts; can reduce the cost of repairs in a major way, in many common repairs.... it is the the labor that is the most expensive cost of getting the job done. We can't make any guarantees but we all collectively, do our best to solve the problems people that post here, are having. Most New Beetle problems; have been experienced by many on this site, thus we can give you advice on how to proceed with troubleshooting, buying, replacing parts and completing the job. Get your car scanned and get back with us on what the codes are!
Autel Hot MaxScan VAG405 Code Reader
http://www.amazon.com/s/ref=nb_sb_n...=vag 405&sprefix=vag+4,aps&rh=i:aps,k:vag 405