Looking back at my first boat, I read a few things on this board that made a HUGE difference for me. They are:
(a) Excellent quality brush (i.e., $15+) with ultra-fine bristles made a major difference. (An expensive brush also gives you significantly more incentive to thoroughly clean your brushes :-) )
(b) air filtration before, during and after varnishing (sounds like you've got that covered.)
(c) any varnish you don't use should be strained before pouring back into the can.

There were some earlier threads on this board about using cloth rags to apply varnish. Perhaps you can try a small section using that technique and see if it works better for you. (Many people swear by the foam brushes...I wind up swearing at them...maybe I've been using the wrong kind as well...)

One final thought: Could there be any issue with the anti-static cloth leaving behind some residue that's incompatible with the thinned varnish?