Just because it clicks doesn’t mean it is good, the contacts inside the relay could be bad. Even if you use a multi meter to check the continuity across the “load” terminals when powering the “coil” terminals, the contacts could still be bad enough to only let a small amount of current thru but not enough to make the starter work.
The best way to test a relay is to swap it out with a known working relay and see if anything changes. But if you can hear it click when testing it off the bike, you should also be able to hear it click on the bike when you hit the start button.
To test if you are getting voltage through it on the bike, check for voltage at the green wire on the starter solenoid when the start button is pressed.
With the other problems you are having, it sounds like your HCI module is bad, or not getting voltage from the PDM module. Check the wiring on the bottom of the PDM and make sure it is all firmly connected.
You didn’t mention if you had done this so I’ll just go ahead and say to first make sure that your circuit breaker (or 40A fuse) to the voltage regulator is good and that you have voltage on both sides of it. The PDM diagram shows power to the PDM from both sides of this breaker/fuse.
Pull all your fuses and make sure the terminals are relatively clean then re-install and check for voltage to both sides of all your fuses.
Checking the HCI.
If you have voltage to the fuses next check for voltage at both red wires on the 12-wire connector going to the HCI (position 1 is from the PDM and position 7 is to the Run switch). Do this with the key on and everything connected, pierce the wire with the point of the multi-meter probe (be sure to cover the pierce later with some liquid tape to prevent corrosion). If you don’t have voltage to position 1 then you have a problem with the wiring between the PDM and the HCI. If you have voltage to position 1 but not to position 7, the HCI is bad. If you have voltage to both then go to next step.
If you have voltage there then hit run button and check for voltage on the red wire at position 7 on the 8-wire connector. This is the power to the ignition and to the coil side (red wire) of the starter relay. You can check this by pulling the relay and checking for voltage at the red wire socket. There should also be a red LED on the ignition module that is on. If you don’t have voltage at either of these then pierce the wire on the HCI side of the connector and check there. If no voltage here after pushing the run switch with the key on then the HCI is bad or the wiring or run switch is bad.
Options
1. Replace the HCI. (I think Badlands and Wire Plus both have a hand control module that can be made to work and still keep the PDM module.)
2. a) Jump the #7 wire on the HCI 8-wire connector to the #1 wire on the HCI 12-wire connector and see if it starts. This bypasses the run switch (and internal HCI relay) and powers the ignition and coil side of the starter relay with the key switch. I’m not sure if defeats the off switch also, but if it does and it starts you will just have to kill it with the key. It also bypasses the safety system that disables the starter when the engine is already running, so if you hit the start button (instead of the blinker) with the engine running it will grind the starter (not good).
2. b) If you also jump the #10 wire (orange) to the #1 wire on the 12-wire connector your brakes should work with the key on.
2. c) If you then also jump the #6 yellow wire on the 6-wire connector to the same #1 wire on the 12- wire connector you will have low-beam headlight. It will not shut off when the starter is cranking, so if you have problems starting, you might need some kind of switch here to help keep the battery output at its best when starting.
2. d) YOU WILL NOT HAVE TURN SIGNALS. Even if you powered them by jumping wires and bypassing the HCI, they would not blink. So if you do all this and have no blinkers, you should not be trying to hit the right turn button and accidentally hitting the start button.