Are you trying to use the stock shark fin antenna's electronics with your 8100?
If so, you will probably not be very lucky with that. I've now seen several different images of the inside of the shark fin antenna, and not all of them come with all 3 anntennas inside. Also, it looks like Toyota used a single cable from the head unit to the rear of the vehicle, then combine it somehow to the 3 antennas in the SFA.
For me, there were indeed 3 antennas in my SFA, one for gps, one for XM/Sirius, and one that I assume is an FM diversity antenna to work with the front aerial. Here's an image of my antennas removed from the SFA:
I did NOT have the JBL system, nor did mine come with gps, yet the antenna was there. Others I've seen online from 4 runners only had one antenna inside, iirc it was the pink-colored chip which I believe is XM/Sirius. Still, another pic I found while researching antennae for mine had two chips, which should have been XM/Sirius and GPS, but no diversity antenna.
Having said that, you say you have the JBL system, which should have come with at least the two chips in the SFA, and if you've found the connector in the dash and you've used the proper adapter to convert it to Pioneer's GPS input, if its not working, it could be either a bent pin on the adapter (or stock connector going into the adapter), or its seeing both antennas and not understanding what to do.
If you rule out the bent pin issue, then in the rear headliner, to the passenger's side of the SFA in the roof, you will find 1, 2 or 3 wires coming from the SFA and plugging into a 3-hole jumper that runs down to the passenger side rear quarter wall. You might be able to pull all three connectors out of that wire plug, then insert just one of them into the cable. See if it works, if not, then pull it out and try the next one.
For reference, this is the 3 wire connector I'm referring to:
FWIW, I too have the 8100nex in mine, and I simply said screw it, removed the antennae from the SFA, dremeled the die-cast plate slightly and stuffed the Pioneer GPS antenna into the housing. It fit perfectly after doing that, I then ran about 3 feet of the wire into the headliner and spliced into the stock gps single cable running to the dash. You have to be very careful and follow some guidelines when splicing RF cables, you cannot just crimp the wires and call it good! It has to be shielded a specific way. I can show you how if you want to go down this path. The only reason why I did this is because Pioneer doesn't have enough cable to make it all the way to the stereo, so I would have had to extend it anyways, and I didn't want to wait for an extension to come in.
As it is now, my gps works EXTREMELY well in the 4runner! I can be in my garage or shop, doors closed (both have a second story above them) and still get almost full signal from all but 1 or 2 satellites!
