Shaggy,
My advice would be to check California's building codes to determine which design manuals may be required to be used in residential/small commercial HVAC design and/or installation. I'm sure CA requires some energy codes to be applied as well as specific HVAC design manuals. ASHRAE and the ICC both have energy codes that are used in some jurisdictions.
In North Carolina, I know that residential heating and cooling loads are required by statute to be determined via Air Conditioning Contractors of America's (ACCA) Manual J and the duct system is to be designed using ACCA's Manual D. I have gone through the former and do not think an ME without a focus in HVAC would have trouble becoming familiar with it. ACCA also has design manuals for commercial applications: Manual N is used for heating and cooling load calculations. ACCA Manual B goes over the Principles of Air Conditioning at a more layperson level than the ASHRAE publications I have come across.
NFPA 90A and 90B are widely referenced standards in the HVAC realm. NFPA 90B applies to small commercial and residential. NFPA 90A applies to larger commercial of combustible construction.
In my studies, the most widely-referenced ASHRAE publication seems to the Handbook of Fundamentals. I have not studied it extensively, but it seems that there is a wealth of information and design information therein. I would guess that the other ASRHAE Handbooks and specific standards would be required for more specific/rare applications, but I could be wrong.
In attempting to reap the benefits of your PE, I think that you are pursuing the correct avenue. There do not seem to be many PE applications for your current area of expertise (i.e., Machine Design). There is no reason why you shouldn't try to become an expert in other areas of Mechanical Engineering--it will not only allow you to take advantage of being a PE but also will allow you to broaden your engineering knowledge. You seem to be taking the correct path at this, starting out in residential and small commercial. It would seem one would have to have mastered smaller projects before attempting large commercial ones.
I'm curious, as I am thinking about doing the same thing you're thinking about doing (but I'm still waiting on my results letter), how did you come along with the opportunity to do some HVAC work on the side (or are you just thinking about it at this point in time?)?