You don't have to pull the motor, I'd say pull the headers though, you'll want the room for connecting the block to the tranny too.
I put the tanny in first, located the tailshaft onto the tranny mount with the bolts all the way through and the nuts on just enough to be secure (tons of room for wiggling). Then i dropped the motor in, and rested it on the engine mounts (left the crane attached for safety) and got the dowels into the block for correct position as well as the TC. Then I got all of the tranny bolts started into the block before I secured the engine mounts.
So basically at one point all of the bolts were in but loose, that wiggle room made it much easier, then I began tighteneing them all a little at a time and did not torque any of them down until they were all "finger tight". Only after all that did I even think about putting the headers on.
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Now, back to the transmission discussion...You have a floor shifter (duh, it's a Mustang right) and you are going to leave the linkage-input the way you have it? It is easy to tell the shift pattern if you can turn it...P-R-N-D-2-1 cannot be "gotten backwards", so if you ca turn the driveshaft or yoke you can easily determine the correct way.