I believe you have to shoot the same rifle over the course, and switching uppers might get you a protest in a serious match.
I think if you aren't going to shoot moly exclusively, then stick with traditional uncoated bullets. If you want to do side-by-side of match vs surplus, then I'd stay away from moly for the time being. Besides, there aren't many people who will claim that moly will yield better accuracy. Most folks I talk to say that it's benefits are found elsewhere.
Personally, I've shot moly for 2 or 3 seasons now in an M1A. I clean w/ Kroil and a nylon brush. At ~300rds, I use solvent and JB Bore Paste and work the barrel back to bare metal. Don't bother starting w/ moly unless the bore is completely bare of copper and other fouling.
I don't see appreciably changes in POI after cleaning, but my first rounds are usually shot offhand, so take that for what it's worth. I shoot high 90's offhand and my call is generally 1MoA or a little better. I usually run a patch w/ alcohol followed by a dry patch before I fire. Anyways, any change in POI due to cleaning would be 1.5MoA, but probably less--I'm thinking 1/2 MoA is a better guess--for the first 2 rds. If starting from bare metal, you might see some variation in the first 5-10 rounds, but I typically am not in a position to observe that personally.
The potential downsides of moly:
Some folks say they get an excessive buildup of moly at 300-500 rounds which will degrade accuracy, but this claim is debated among the guys who shoot it a lot. This is the reason for the JB paste cleaning I do, but I haven't left it in longer than say 400 rounds to confirm or discount this statement.
Some folks say that it attracts moisture and can lead to pitting. This is also tied in with concerns that sulfuric impurities in the moly will lead to localized acidic areas, again leading to pitting. My bore is definitely pitted, but let me also say that I had a saltwater aquarium for 2 years that was evaporating 1-2 gal of water a day, so that would definitely be a factor. Personally, I think that moly and a moist environment make a situation ripe for corrosion. My recommendation: if you shoot moly, get a coat of oil in the barrel ASAP after shooting and keep it there until you're ready to shoot again. If you do this, you shouldn't have a problem. BTW, I wouldn't use Kroil or other penetrating oil as a rust preservative. The protective barrier that it provides against O2 does not remain intact for more than a couple of days IMO/IME.
Upsides:
Quick cleaning & longer period of accuracy between cleanings. It will give you lower velocities, but the corresponding decrease in pressure will be more. This can be used two ways. First, keeping the powder charge the same will yield a longer barrel life (Tubb estimates something like 20%). Second, increase the powder charge and eventually get higher velocities for the same pressure that you would have with uncoated bullets.
Ty