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The proper way to use moly is to COAT THE BORE before shooting any moly bullets. Clean the bore down to bare metal. How you do this is up to you. Personally, I avoid using abrasive cleaners like JB Paste in my precision barrels. Be warned that the use of abrasives in some premium barrels may void the warranty. With a bore scope it is VERY easy to see if such abrasives have been used on a bore, as the rifling will no longer be sharp edged. Use a powder solvent and copper remover to ensure you are down to bare, clean metal. Finish the cleaning with something that removes any oil from the bore. I finish up with a cleaning using MPro7, or a good flushing with everclear. I also remove my barrel to coat the bore. On an AR-15 this is easy and it makes everything much easier. I re-coat about every 1000 rounds - not my plinking rifle.
Once you have a bare, clean, oil-free bore, use Ms.Moly to coat the bore. Ms.Moly is very easy to use. I have no stake in the product, but do heartily recommend it. I spray Ms.Moly on a cotton bore swab until it is well soaked and almost dripping wet. Swab the bore, and let it dry for an hour or so, repeat, dry, repeat. That's 3 coats with drying in between and after. Send a few tight patches down the barrel after a few hours or overnight of final drying time, then follow it up with a well oiled patch or two. I keep my bores pretty wet between shootings, then run a tight patch before shooting, and shoot a couple of fouling rounds before shooting for score.
Some reports have been made of moly pitting barrels. This appears to be a problem with chrome-moly steel barrels and moisture. I have not seen any problems with use of moly in my stainless steel barrels. For more information see Varmint Al's website. I think Varmint Al's is one of the most interesting sites on the web.
Shoot ONLY moly'd bullets out of the coated barrel. Little to no fouling will stick to the bore and what is left on the surface of the moly can be pushed out with a few patches. If you ONLY shoot moly'd bulets the bore coat will last a VERY long time, because you now have a moly/moly interface rather than a moly/metal interface.
People have been using moly incorrectly for a long time. They have shot moly'd bullets out of non-moly'd bores and expected some magic to evenly coat the bore. Instead all they do is make a mess of their barrels. They have shot non-moly'd bullets out of moly'd bores and expected to get the benefits of moly. Instead they have damaged their bore coat by randomly stripping it out.
MOLY IS NOT A PROTECTANT.
Many have erroneously considered moly a protectant. It is not. Moly is only a dry lubricant. A moly'd bore is not immume to moisture. You still need use some sort of bore protectant, like CLP or Kroil, to protect the bore from rust and the like.
Although I use Ms.Moly to coat my bore, I do not use it to coat my bullets. To coat bullets I use an impact system that employs powdered moly, steel shot, and a vibratory tumbler. This is described elsewhere on this site.
Used PROPERLY moly will ease cleaning and may extend the life of your barrel. I personally believe that it increases my precision and consistency leading to smaller groups, but I'll not make the claim in general.