What you call the 2 upside down bolts are dowel pins that are straight and smooth below threads. The threads were to put a nut on them to remove. No mater they just go through gear box and into transmission cover. If you have the bolts out of gear box it will come off with cover, or the gear box should pry off and pull the dowels with it. If you have all bolts removed from cover top, remove the ones from brake covers that screw into transmission top. Some dowel pins you can't see until top is off is all left to stick to. If you raised the rear of cover very much when trouble started the shifting forks may be bent and causing tractor to try and go into 2 gears at once. In transmission top just below shifter look for 2 expantion plugs, they hold pin in and pin holds gear shift. Remove gear shift and look down hole and line slots in shifter rails to center position. See if that frees transmission. If shift forks are bent it may not help. Or as you said could be something else messed up.
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