I just did my second auto-to-manual swap, but this time I left a stock engine in the car so it runs again.
A few notes:
I was wrong about where the clutch line is supposed to go--it goes through a large area behind the frunk in the same place as the brake lines. However, I found it easier to put it where it doesn't go, which is through the same hole as the '92- speedo cable, right behind the power steering pump. With some help and a second jack to hold up the gas tank, the stock location wouldn't be hard to get to.
For the next two, you'll be splicing into the harness-side connector that goes to the shift lever on the old transmission. Here's a diagram of the connector, but this one is the tranny-side connector, so 1/4, 2/3, 5/9, 6/8 are all reversed when you're looking at the harness-side.
To wire the clutch safety switch: run two wires from the lower switch on your clutch (the upper switch is for cruise control shutoff) to the connector that used to be on the auto transmission. The wires you splice into are the largest ones, and are black and red (numbers 2 and 3 on the diagram). On the front of the connector, they are the widest holes as well. I ran the wires behind my gas filler pipe, behind the heatshield, through the shift cable grommet, under the center armrest, over the brake and clutch pedals, and down to the clutch switch.
To wire the reverse lights: run two wires from the connector on top of the manual transmission to the same connector you spliced into for the clutch safety switch. It's pins 5 and 6 on the diagram (remember that the diagram is backwards from the connector you are splicing into), and one of the wires is black and yellow--can't remember the other one. Note that this also turns on the reverse indicator on the gauge cluster. I thought that was pretty cool, probably because I'm a geek that way.
Before splicing anything, you should always use a test wire to make sure you've got the right ones. Just stick one end of the wire in one 'pin', and the other end in the other 'pin'. For the safety switch, it shouldn't turn over until you jumper 2 and 3. For the back-up lights, it should turn on the reverse indicator and the back-up lights, but only when the car is in the on position (maybe acc. too). Just don't jump the wire between 6 and 2 or 6 and 3 (you might short something). If you want to be safer, put a small (5-10 amp) fuse in the middle of your test wire--since you're turning on relays, there shouldn't be a lot of power going through, and you'll avoid burning something up if you somehow get the wrong ones.