nice work, getting that damn pedal assembly all up in there and mounted is probably the second hardest part of the swap with bleeding the clutch system being the first if you have never done it before.
now some other tips on the swap.
-the clutch position switch, either grab the switch from a junkyard or get a new one, it mounts on the rod of the master cylinder. The wiring is all there tucked up in the driverside with a jumper plug in it, all you have to do is remove the jumper and plug it into the clutch position switch. With this you will also need to splice together two wires under the truck in the automatic transmission plug pack (like 16-pin or something). You will want to splice together the pink and teal/red wire. This is for the park/neutral sensor in the auto tranny which the manual obviously doesn't use because it has the clutch position sensor. So you need to wire these two together to bypass whats nolonger there.
while you are under there you can also wire in the reverse light switch (which you will need to cut off a manual truck, it is a 2 wire switch that plugs into the top cover of the tranny). The wires for it are purple with an orange stripe in the automatic wiring harness.
-make sure you have the manual tranny flywheel bolts and the tin seperator plate for a manual tranny as they are different from the auto ones. The starter may also be different depending on the engine and years.