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Went under, found the starter was loose. I took it off and saw the top mounting hole has threads, the bottom one doesn't have one. I tried to install the top hole first, but keeping missing it and won't go in and hold. Do I need a longer bolt or something? I thought I had the wrong stranger, so I went back to the place I got the rebuilt starter from and compared to the old one and it was the same. The bottom one is ok, but keeps popping off if I bolt the top one while the bottom one is in but not tight, just enough to hold the starter.
If there is a shim in between the dust cover and the starter, that might be what's throwing you off. I had to use a shim because my truck kept eating starters. I had to drill the hole slightly to get the top hole to line up correctly. As for the bolt, maybe they got mixed up and someone put a short one up top. But if all else fails, get a longer bolt. Hope that helps.