What else should be done during timing belt replacement?

[kiltman]

The orange LED on the switch pad goes on and off with the switch, but it doesn't engage.

That’s a different switch than what I have. Mine has three green LED lights. One in the middle that lights up when the system is turned on and the other two light up the on /off and set /resume switches.
I would check the trouble shooting LED light in the servo. It will let you know if the brake circuit is functioning, if the set button is functioning and depending what is determining the speed sensor. ( if it’s just the tach indicating the speed, it may not give you feedback on that) The common place for installing the servo is by the back of the left tip over bar. To get at it, the underbelly cowl has to be removed and the left middle cowl has to be removed.
Your orange light might still come on when you press the set button but if there isn’t enough vacuum to the servo it might not engage, or the brake circuit isn’t functioning.
To insure I had maximum vacuum, I used one way valves and tees hooked up to three of the carburetors, then plumbed to the reservoir tank. I installed my tank in the Tail section, some made a homemade tank that they fitted under the bike near the kickstand. If that bike is a California model or ABSII model there is a charcoal canister near the kickstand instead.
That engage light will probably also light up if the cruise cable is disconnected from the throttle linkage, you might be able to see that if both the shelter and the seat are removed. The cable from the servo may go underneath the bike to come up on the right side of the bike and there may be a lever attached to the bell crank of the carburetors, you might be able to check that is functioning.
You could also try substituting the cruise control switch with a similar one you used on your 750 see if that’s the issue.