this was the route I went with last week.. The bolt wasnt located, so it was deemed "stuck to the bottom"
replaced the bolt, and went on the merry way.. not 15 minutes later, the tranny found the bolt I could not -- and promtly shot it through the case... Enter new scenario, $2000 and a new tranny to install.
here is an issue you may run into. The trans for a 99 is no longer sold as a complete unit. However, the 2001 unit is. the difference? that shift tower. Where the linkage mates to the trans is different, so you will need to get cables from a 2001. (dont know yet if they attach at the shifter the same)
Ford quoted me 3500 to get it done. Breakdown: trans for 2001 1700, 600 core charge. since the case is shot, it is useless as a core, so 2300 for the trans. approx 100 for cables, and 1100 in labor. I told the dealership to go pound sand. With a little searching, I found a Euro Spec trans from Bat (dont call, i got the last one) for 1550 + shipping. no core required. My mechanic said he will do the whole swap for about $350 plus the cost of the cables.
I seriously recomend that if you havent found that bolt, pull the trans, take the tower off and shake the hell out of it while its upside down.. you may get lucky enough to have it fall out the way it fell in..