Re: jonhson 75 stinger, and powershift 2 controls
Tilt/trim wiring is typically blue (up) and green (down). What year motor we talkin bout?
If it has factory tilt/trim with a switch on the control box it's probably a rocker switch at the top of the shift/throttle control handle.
Older models might have aftermarket or dealer-installed OEM tilt/trim with the switch on the dash in which case the tilt/trim wiring is in a separate harness.
A previous owner might have replaced one of the original wires with orange.
Or, it could be a faded red wire that appears orange.
On routing the throttle & shift cables, you mean "starboard side" --now you're a boater, learn the terminology

-- on my boat, they run through the starboard gunwale, make a 90? bend at the splashwell, pass in front of the motor then make a complete 360? turn to enter the front of the cowling. Don't worry they won't bind. Any case, impossible for us to tell without seeing your setup -- post some pics, we'll take a look.
If your motor has a telltale, you should get a pretty good pee stream any time the motor's running. Were it mine, I'd rebuild the water pump now -- that way, you'll know how strong it pees with a brand new impeller. If it doesn't have a telltale, you know it's working when because the overtemp horn isn't sounding a constant tone. When that alarm sounds, it means "shut 'er down like right now!"