I have tried various ways to get the sub to play properly but the HK wiring is the problem I believe.
The Alpine HU currently is connected via a harness adapter to make it work via the original wiring. So the signals are all running via the HK amp/crossover. So even though I have a second amp (for sub only) with RCAs from the HU >amp>new wiring to sub; the subwoofer is not getting this signal, it is still only going via the original wiring.
So am thinking to just run new wires for the speakers and run it directly from the Alpine HU and and new amp. For now I will run the rear speakers and front speakers from the HU only (tweeters in doors will be disconnected) and run the JL sub via the amp. Will need an active crossover, at least 3 way for now too.
This way is simple and the original wiring remains intact if I wish to return to standard one day.
Later on will get around to upgrading the rest of the speakers and upgrade/add another amp for whatever replacement speakers I put in the rest of the car.
Some pics:
HK amp/crossover:
Wiring in and out of HK (plenty of it for just 9 speakers!):
The 4 wires that powered the original HK sub. I used 2 of these (one of each colour only) to power the JL sub:
RCA outputs from ALPINE HU