The serial numbers don't match because the "hard parts" like the trunions, barrel, carrier, bolt, etc. all came from an original AKM rifle made in Romania, Bulgaria, or somewhere like that. That rifle could not be imported to the US as a functional machine gun (or "non-sporting" semi-, even) so the receiver of that rifle was cut up and the parts were imported to this country as a "parts kit." The rifle was then reassembled on a new (assumedly) US-made receiver, which has it's own serial number. That's the gun's official serial number of record now, by the way.
On an AKM, the bolt rails are spot-welded inside the receiver shell. Lining these up is sometimes a trick, and it sounds like these never quite fit right.
As a rule, you ALWAYS adjust the sheet metal receiver. NEVER the trunions, barrel, bolt, or other "original" part. Put another way, those pieces came out of a rifle that (presumably) worked great before it was cut up and sold as a parts kit.
Grinding on the trunion or bolt lugs is just not a good idea. Very much like cutting off your toes because your new pair of shoes doesn't fit right. Keep the original parts intact (toes, trunion) ditch, replace, or modify the new stuff that doesn't work with them (shoes, receiver).
The easiest answer is to turn the rifle over and use a flat-tipped large punch or some such tool with a large hammer to tap the bolt rails upwards right behind the trunion and try to bend them up enough to make that transition smoother. 0.04" sure isn't much to bend that thin sheet metal. In fact, tweaking the rails (both the top rails and bolt rails) is a normal part of buiding one of these things. Whether the rails are perfectly straight, level, etc. in the receiver isn't really all that much of a big deal as long as the bolt rides on them smoothly and can easily find it's way back into the trunion to lock up. If you grind on the bolt lugs, chances are you're going to screw that up and possibly kill the rifle. But, I'd bet a LOT of money that you can bend the rails gently, far enough to make the gun run beautifully. Just clean the burrs up where the bolt and or carrier has been peening and call it good!
If you CAN'T get it to work and decide you must replace the receiver, get a Nodakspud receiver as they're just plain wonderful. Disassembling an AKM down to its constituent parts really shouldn't take more than an hour. Re-building it on a new receiver is about a 2-3 hour job if you've got adequate tools for pressing the barrel & pin, and for setting the various rivets. (Note that the same method won't work for setting all the rivets. Some are trickier than others and will require a tool such as a modified pair of bolt cutters to reach into the trunions and squash them correctly.) Just remember, due to all the manufacturing tolarances and slop with all the AKMs from all those factories all over the world, even with a great receiver, you may have to do the exact same thing to make the gun run...definitely try bending the rails first!
If you really don't feel that you can do the job correctly, quickly, and/or cost effectively, advise your client to contact any of the builders who specialize in making AKs.
AKfiles.com will help you a lot in figuring this stuff out.
Good luck!
-Sam