Sub Not Waking Up

Check if they turn on and off manually. If they do not turn on automatically check for trigger voltage. The turn on signal is nothing but a constant voltage so use a volt ohm meter to check for that. Does not matter what it is, if there is any voltage at all they should turn on. If it was one sub I would say maybe a sub has a problem. But when its two subs its just way unlikely they both went bad at the same time. Either you hooked up something wrong or the Yamaha is not triggering them. In this day and age everyone is so easily triggered that’s hard to believe, I would cherish the subs for that reason alone, that they are hard to trigger. Not to mention the cool factor in having subs that aren't woke. Seriously though, don’t be triggered, pretend I didn’t say that. Disconnect the trigger, it is silly (in every sense of the word) just turn the subs on and leave them on. That’s what I do. But then I hate being triggered, even if it is just an amp.

The Yamaha is not triggering them.  When I go through the YPAO process I can hear them kick on and the light comes on.  This does not happen when just listening to them.  I rewired them using the speaker level inputs coming straight from the amp.  This means I cannot use the Yamaha to adjust sub level but at least they work and I can adjust the volume on the back of the sub.  

I have no idea what setting to change in the Yamaha to get it to trigger the subs.

I'm not familiar with that particular receiver or those subs, but with most receivers, there are ways to activate or deactivate the subs and also the listening mode you've selected may affect whether the subs are active or not.  Double check all that.  Worst case, just leave the subs turned on.

"I rewired them using the speaker level inputs coming straight from the amp."

Try using a regular subwoofer cable and see if they are triggered then.

@mobiusmu 

I know this may seem elementary, but do your subs have gain control? Make sure they are turned-up if so.

Using YPAO in the receiver itself sets volume/gain within the receiver, yes, but some have found if the gain is not turned-up at the sub itself there could be an issue with it triggering on at ‘start-up’ volumes, or, not enough initial gain to trigger it. Once the volume is adequately turned up at the sub itself, then adjust via YPAO, or within the set-up settings. Personally I have never found the YPAO settings to be adequate for correct sub settings via LFE when I used to run my sub that way. I always manually adjusted its gain within the receiver settings with a meter.

@mobiusmu 

I know this may seem elementary, but do your subs have gain control? Make sure they are turned-up if so.

+1
Or use a 12V trigger outlet for the subwoofers.

https://dlidirect.com/products/iot-power-relay

most probable problem:
a)You probably have the volume control knob on the sub way up.
b) YPAO may have compensated when it does it's level matching with your speakers by turning the level way down for the sub. The signal the receiver sends now is insufficient to "wake up" your specific sub during playback.

Solution:
Start turning down the volume knob on the subwoofer unit such that YPAO is setting sub levels to +3dB or more when it does its level matching. The receiver should send something big enough/sufficient to "wake up" your sub. 

Actually YPAO is notorious for setting the sub level via LFE too low regardless of the gain setting at the sub, which as I said, thus I always adjusted it manually when using LFE with my receiver. Albeit I don’t do that anymore.

But yes, as I also said, most probably the sub gain is set too low.