I changed my car from auto to manual about 13-14 years ago and I used the original tailshaft. That's one thing you don't have to worry about. Remember to put in a "loop" harness for your shift harness to the inhibitor switch that was on the auto. If you dont. She won't crank and you may get cranky.
This harness comes from your auto to a connector just under the centre of your tranny tunnell just behind the cylinder head. 2 bullett terminals and a short length of 5mm wire is enough to make the "loop". 
When you want to cut a hole inthe floor, and the engine and gearbox are still out, measure the distance from where the box joins the engine to the centre of the quadrant box,(that's the 4 bolt housing for your gearstick), and take this measurement from where the tunnel starts on the firewall back towards your handbrake. This should give you an approximate position to cut your hole. Bearing in mind that the tunnell on a auto has mount points for your auto shifter and is lower. The tunnel from the heater blower mounts forward are all the same. You may have to nibble a hole a bit at the time for the manual quadrant. Also allow for the "throw" of the engine and gearbox and does not foul the floor.
If you were lucky enough to get the rubber boot with stick, your next part of the project is to make a hat to go over the tunnell to retain the boot and keep the fumes out and and any carpet etc. from fouling. If you haven't cut out the old auto mount points, use them to mount the hat. I converted my sedan to a GT style tunnell and I may still have the hat I made. Will endeavour to find it and post a picture up so as you will know what I'm on about.
Dave.
