Diff cover screws are 5/16"-18x3/4", just like the "corner" screws on the oil sump. Probably come out of the same bin at the factory, if it's a 35C.
My money's on this or an inspection cover bolt, though I don't seem to recall those being serrated.
This is on your 91 right? Looks like bolts for the inspection cover (unless I'm misreading my catalog/diagram) are 3x M8x1.25x20 2x M12x1.75x35mm (those are the big honking 18mm head ones) and 1x M8x1.25x30mm. So if they're metric, that's probably where they came from, if they're SAE I'd guess a diff cover bolt or something else. Could also be one of the bolts holding the various cable straps onto the sides of the block, IIRC those are almost all non serrated 5/16" and 3/8" bolts though. Maybe a distributor hold-down bolt (1/4-28 1.625" long, says the internet, which seems wrong to me. Part number is 6033 479 if you want to verify yourself.) The short bolt holding the oil pump to the block is a 5/16-18 that is either 3/4 or 7/8 long, not sure which, and the 4 bolts holding the cover plate onto the oil pump housing are 1/4-20 1/2" long.
It could also be any of a handful of short stubby metric bolts on top of the intake manifold holding various brackets and the fuel rail down, though I don't recall any of them looking like that.
In any case, I'd check the oil pump very carefully, make sure both the long and short bolts are present and the 4 bolts holding the cover plate on are installed, and then button it back up and forget about it.
I didn't notice any bolts like this one holding the inspection cover on, just two really small ones and two really big ones, but maybe this one is supposed to be there too. I'll have to check later tonight.
What's up with those huge 17 millimeter bolts & nuts on the inspection cover anyway? They don't seem to be doing anything the smaller machine screws aren't already doing yet they're beefy enough to be control arm bolts...
I thought they were 18mm heads? That's what I seem to recall using last time.
Either way, I believe it's because the bolt pattern for the bellhousing was originally designed for a V8 (doesn't the 4.0/258 share a bellhousing pattern with the old AMC 304/360/390/401 in '72 and later? I've been lead to believe so though I'm not certain) which could have mounting bosses much further below the crankshaft as it's a 90 degree V block instead of an inline. Either that, or they are intended to have pressed steel braces bolted to them, as the chryco V6-239, V8-318, and V8-360 have - the braces bolt to the lower bellhousing bosses as well as to the engine mount pattern and (at least on the Dakota) to the bracketry which attaches the IFS diff housing to the frame.
edit: verified bellhousing pattern is the same, '81 CJ with a 6 or 8 cylinder engine uses the same part number auto trans w/ bellhousing. Still haven't verified what the lower bolt holes are for and can't find a pic of the back of an AMC V8, but reasonably certain...
edit2: AMC V8 doesn't appear to have block skirts that go down anywhere near that low, so I'd put money on them being intended for attaching pressed brackets to hold an IFS diff and/or stiffening braces to the engine mounts, which were then never needed on the XJ.