The FSMs have been back up for a while now. They were taken down the other year, but that's all been sorted. The screenshots I posted were from accessing the 99 FSM that day. It does appear that conversion doc is now no longer available, though.
Since that other guide already shows how to bypass the P/N Relay in the box (you're basically just jumping the connections), the easier route to incorporate the clutch switch would just be to put it on the same circuit as the brake switch above the pedals. The ASCD module is just checking for any opening on the circuit, so if you add another switch there it won't know the difference.
As for that relay bypass, if you want to keep the installation clean (and safe), you could pop open that relay and solder the connectors in there instead of just jamming wires into the open relay port in the fuse panel. Either way, make sure the wire is sufficient gauge, otherwise you're just putting a filament in place. Other way is to just make short jumper wires using crimp-on terminals.
The FSM also confirms the following:
Pin 18 is the signal to the Cruise lamp on the dash. The TCM also uses this as an input signal/switch that CC is engaged.
Pin 12 is a signal to the TCM to turn off overdrive. This specifically occurs when the vehicle speed drops to 5 mph or more below the set speed, allowing the TCM to drop the transmission out of OD. Once the truck is 2 mph over the set speed, then the signal is turned off and OD use restored. The vehicle speed is detected by input from the gauge cluster ("Unified Meter Control Unit") on Pin 7, and speed is adjusted by the ASCD's control over the ASCD pump (Pins 8, 9, 10, and 14)
That said, removing the TCM should have no impact on cruise usage, and wiring up the switch looks super simple. I'd bet if you can get the under dash wiring for the switch, you could just pop the terminals out of the harness and make it look like it was always there.
For reference, you can find this info on EL-163 in the 99 FSM Electrical System. The first few pages cover the System Description, Schematics (shown above), and the Wiring Diagrams.