Reclino, I haven't used Brownell's Moly finish, but I have done two handguns with a similar finish, Norell's Moly-Resin.
I disassemble the gun entirely and coat all parts except the springs and anything too small to easily handle. These finishes go on very thin, unless you intentionally build it thick, so closely fitted parts will go back together easily. Anything that fits tight will loosen up just fine after shooting a few rounds through it. You'll find that the gun needs much less lubrication after applying the finish because it is self-lubricating.
The "spray-and-bake" moly/teflon finishes are highly resistant to chemical reactions but are about as resistant to physical wear as any parkerized or blued finish. They will scratch and show holster wear after a period of use. However, they are trivial to touch-up yourself. I've found that letting the parts sit for a week or two before reassembling allows the finish to fully cure and harden making it less succeptible to wear.
You can find a good description of how to apply Moly-Resin, and where to buy it, at
http://www.flash.net/~gavin1/refinish.htm . The Brownell's Moly finish is likely applied pretty much the same way.
The method I use is to first dissasemble the gun and degrease all parts with Simple Green. Then place the parts on an old, clean, cookie sheet and heat them in an oven at 225 for 10 minutes. The instructions recommended at least 150, but I found that the higher temp made sure the finish dried as soon as it hit the parts. Then, take the cookie sheet out of the oven and immediately spray the parts with the finish using a cheap airbrush. Turn the tray with your hand while spraying the parts lightly from many different directions. Then flip the parts over (if warm enough, they should be already dry to the touch) and repeat covering any exposed metal. When completely covered, return the parts and the cookie sheet to the oven to cure at 300 for 1 hour. If you mess up anything really badly, just sandblast off the finish and reapply. For small imperfections you could just sand off a small area, re-heat the parts and reapply.