I'm in a similar position to the OP, albeit in a different part of the world. There is right on both sides of the argument: specialized knowledge and equipment is required to safely maintain a certified GA aircraft, especially one in IFR category. (And the kit required for some of the maintenance and certification on the more advanced systems is likely beyond the means of an individual aircraft owner). By the same token, I've seen (and solved) some pretty bad engineering issues by avionics shops.
An approach which worked for me was to get know the techs at one of the better companies, then work with them in diagnostics, installations etc. In Australia at least it will ultimately have to be the licenced tech that signs off new installs, instrument and transponder checks, etc. Fortunately, a lot of expensive tech time still goes into hunting basic issues and with your own comms knowlege and basic equipment, you can make a big difference to the bottom line.