Studs and nuts are the way to go but you will have to decide if there is enough threads to hold. It doesn't surprise me that the hardest bolt to get to has some bad threads. The first few threads are bad probably from cross threading in the past. Bad threads are at the start of the hole so a shorter bolt won't do any good. You need a longer bolt but not too long. Screw a longer bolt down by hand or with very little effort with a socket. Don't force it or you will strip what threads you have left or worse, cause a crack. If the bolt head doesn't clamp the cover down tight you will need some washers to take up the gap. Studs would work best. If you go studs, remember that they don't need to be screwed in tight to work. You can screw them in 3 or 4 good turns and the tension will keep them tight.