I also have an August '42 GPW as well and as you know, none of those features were present when delivered from the Factory; (blackout light, Trailer socket or Jerry Can holder). All were added as field mods including the reinforcing plate right over the rear star on mine though the rear panel reinforcing braces were never added. As you know, these would have been done by soldiers going more or less by the modification package instructions.
The blackout light on your jeep may not have been the Tombstone, but could have been a later light guard which I believe has a different pattern, (or the fender simply could have been changed out from a later jeep.)
If it were me, all of these holes are evidence of your particular jeep's history and I'd try to preserve it as closely as possible as long as it serves functionally. I'd use your new Tombstone guard drilled correctly but if the other items work, I'd just use them as they fit, knowing that these field mods were done not as a factory would have done them, but as they were done by a GI in the motor pool. That gives it some real character I think.
1941 MB 105444
1942 GPW 61323
1944 Converto Dump