If your 1950 3100 is like my 1949 3100, the inner fender wells and the brace at the bottom of the fender "locate" the fenders at the cab. On my drivers side, there are 3 nuts "welded" to the toe board that are used to fasten the inner fender to the cab. On the passenger side there are only 3 holes. You mention that the FENDER bolt holes were bondo-ed closed. If the INNER fender are still "original", you should be able to locate the fender holes with the inner fender hole ("nut holes"). If bondo was actually used (not welded shut) to fill the hole, a small magnet could also be used as it will not stick to bondo.
Please note, these old trucks need a LOT of "massaging" to make them look right. The fenders might need to be bolted tight and correctly positioned before you get concerned about the gap you are seeing now. Good luck!!


Always get a 2nd opinion, especially if I am the source of the 1st opinion.