Well, got some pictures and junk. For anyone doing this... if you pull the M5OD from a 4.0 rig, make sure you KEEP or get a master cylinder from a 4.0 rig as well. I learned the hard way. I couldn't remember how the quick disconnect fitting at the slave worked at the JY when I pulled the tranny, so I cut this line. Terrible idea. I then proceeded to pull a clutch assy. from a 2.9 rig with an M5OD. Worked just fine as far as fitment went... but the male end of the quick disconnect was of a smaller diameter than from the 4.0 slave! Darn! So on the hunt I went... you know how many places just cut that line?! In the whole Interior or British Columbia, I found ONE. ONE! It was $135 new from Ford... ouch. Anyway, on with the pictures!
Here is the rough cutout in the floor covering. Got the floor plate from the Explorer I pulled the tranny from. Having a 3" BL, that rubber bit doesn't quite fit proper so I had to trim it. Also, the boot doesn't fit in the stock location, but I'll show you my solution to that when I get it finished!
Right here, on an auto rig, there is a little cap covering this hole. Simple. The two bolts are a ROYAL pain to get at... but they are 10mm and I used a buttload of extensions to get at them. Normally the inner fender is in the way, but for some reason mine wasn't and this slid in perfect.
Clutch interlock wiring. This is tucked up in the wire harness just behind the e-brake assembly. Note the cap on mine... that is to bypass the clutch interlock switch as an auto machine doesn't have a clutch. I left this in place as I had to drive w/o a clutch for a few days. 
Here's the wiring harness(es) that you'll be looking for to jump the Neutral Safety Switch in order to start your truck after the swap. They are just below the coolant/bug juice jug on the driver side inner fender.
And finally, here's the two wires you need to jump in order to bypass the NSS and start your truck. Simple! Red and light blue wire jumps to the solid pink wire!
Didn't really get a lot of pictures during the swap, but oh well. Was too busy trying to get it done! Haha. I'll take more pictures in better light another day.
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