I was not careful enough in my description, so sorry for the confusion. To clear a couple questions up:
There was no actual "boom" noise, I was using that word to imply how suddenly and unexpectedly it happened.
This issue happened 3 times that day; each time I was able to push the shift rail back where it needs to be and drive on without issue.
Yes, I was in third shifting to neutral when this occurred. I am fuzzy on which gear it ended up in, since I was in traffic and harried trying to get it off the street. Once parked, I was focused on getting the rail back and driving. It was probably in third, or some in-between... not neutral... I had to depress the clutch when we pushed it out of the way. Not 1st or 2nd, since I could not drive it.
After looking around the web yesterday it seems likely that the shifter nubs or the shift rails are too worn to positively engage properly. I will pull the shifter tonight and get a pic. I wont be able to pull the shifter housing until this weekend.
When I bought this trans it came out of a very nice 35 ford in orange county... the owner had just swapped a 24 stud with trans into his car. All the gears were intact, not chipped, etc as we turned over the shaft with the tower off.