Do you honestly get different vacuum readings from the gas filter (assuming it's clean/new) and the AC or brake line fittings? They shouldn't be different.
You answered it: Most run the original Gas Filter - It just has a thick wire mesh in it and every old one I've taken off is occluded by 35 years of s***. I've never tried to clean one as they're inexpensive. The vac probably pulls down to full after a bit, but again, that component is cheap and available.
I wish someone made a 1/8 BSPT Vacuum tree to replace the finned-cooler for the brake booster/idle up vac source. Be nice to have something with 4 or 5 ports as well as a 10mm (?) one for the break booster vacuum.