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1989 Ford F150 T18 Transmission problems

Hi all, I’m working on my 89 Ford F150. It’s got the T18 4 speed transmission in it. Putting the truck in neutral, we removed the shifter lever to inspect the “pin” that helps control the lever wobble. It was worn down so we drilled the bore out a bit and fashioned a new pin. We needed to drill the top of the transmission housing out a bit to accomodate the new pin so we removed the top of the casing. I believe that’s where we’ve run into a problem. I’m now seeing alot of instruction that for removing the top of the case, you’re supposed to throw it into 2nd gear. I was also told in several places when removing the lever to keep it in neutral. The lever is separated from the top casing and now nothing wants to go back together. The shifter lever doesn’t want to go into the top case( I believe this is because the shift forks shifted out of neutral and we need to reset the gates). The top case won’t go back into transmission (at some point the transmission got itself into gear, we managed to pop it back into neutral. We know this because we have the truck tires blocked off by cinder blocks and it now rolls like it’s in neutral. I guess my question is, do we just need to pop the shift fork gates into neutral and everything will line back up, or am I going to have to play a weird game to shift the transmission into 2nd gear while keeping the lever in neutral? I’ve included an image of the inside of my transmission and a photo from Jeep forums regarding alignment of the gates.