Which would you recommend? A HEPA filter (if so what brand/model) or similar efficient system, or a gas mask (like a K-1 or MSA full-faced with 40mm NATO threaded connectors) ?

I could use either one... the gas mask in case the SRHTF (Shit really hits the fan) and for practicing at the range, or a HEPA/filtration unit.

I want to isolate myself from possible airborne molds/mildew and see how I feel in 2-3 weeks. The way I see, a filter unit is going to run $400-$1000. A new mask is about $200. The filters aren't good for long periods of time but I figure I'm not in NBC warfare so an inefficient filter is going to at the very least get rid of the allergens when it's 1-2 years old.

I could see an allergist but I suspect several copays, and several prescription meds later, I'd be in the same exact situation as I am now... At least with a HEPA or gas mask, I'd have a cool toy afterwards.

Get the gas mask. If you've never worn one you'll love the feeling I'm sure . You might also want to consider a scott pack, (thats the bottle and mask firefighters wear) cumbersome but chicks dig firefighters and you could pretend to be one. I'd try the doc though, flonase and antihistamine might be a better solution.

Umm, here's a cheap suggestion.

3M 6000 series half mask respirator (air purifying) with P100 or N100 filters.  P100 or N100 = HEPA level filters.  You can typically find this at a hardware store like Home Depot or Lowes.  

I work with an Electrician that is allergic to just about everything and his asthma is also very bad.  He wears one of these when he cuts the grass or weed eats and it makes a big difference for him.  These types of filters typically block up to 99.97% of airborne particulate dust and depending on the amount of exposure can last a few days to weeks.  I would recommend changing them out at least every other day especially if used in a moist or humid environment.