LK,
Nothing's wrong with the surplus ammo - a lot of surplus of all types (5.56, 8mm, 7.62x54R, .303, etc) dates back to the '40s and '50s and is just fine. A lot of 7.62x54R is newer stuff from the '70s and '80s.
On a Mosin-Nagant, serial numbers are located as follows:
- On the receiver, below the year stamp
- On the bolt
- On the buttplate
- On the magazine floorplate
- Possibly on the stock
A mismatched Mosin will have the original serial number crossed out either by a stamp or by an electropencil, and a new "matching" serial will have been stamped or electropenciled onto that part. It doesn't matter any except for collectability, although you should headspace a mismatched bolt.
A gunsmith or shop owner can do it for you if he has a set of 7.62x54R go/no go gauges, but unless Mosins are really popular in your area he probably won't - mine just told me to tape two layers of electrical tape over the bolt face and see if it closed. If it doesn't, it's fine.
You can also buy the bolt tool which includes notches for checking firing pin protrusion as well as being a handy screwdriver for taking the gun down.
When a Mosin is rearsenaled it's reblued if needed and any needed repairs to the stock (for cracks, etc.) are made. To signify it was rearsenaled they stamped a box with a slash through it on the stock and the receiver - looks kinda like [/]. It can be a pretty light stamp and hard to notice, but it should be there. No mark, no rearsenal - it's all as original.
Mosin bolts (among other parts) are often mismatched because the Russians, when cleaning their rifles, would take 'em down and dump all the parts into one big communal tub of cleaner, then reassemble their rifles with the first parts they grabbed out of the tub, matching or not.
There is a noticeable difference in appearance on pre-war and war-year rifles - my '46 is a ton smoother than my '44. The '44 has tooling marks all over the exterior and the receiver tang is misshaped, looks like somebody finished it with a fine file. It's not that bad, but if you're looking for a "really nice" Mosin (some here are crying oxymoron right now) go for a pre- or post-war year.
Regarding counterboring, since I imagine you don't know - if the rifling towards the business end of the barrel was damaged enough to affect accuracy noticeably, the rifle was counterbored during rearsenaling - basically, the barrel was bored out down to undamaged rifling. My '46 is counterbored and very accurate. You'll be able to look down the barrel from the business end (with the bolt out, or at least open, of course) and see if it's counterbored - the first 1-3 inches of the barrel will be a larger diameter with no rifling, and then it'll "step" down to a smaller diameter with rifling.