The sub feed is just tapped off of the rear speaker wires so removing it won't affect anything else.
Since it is hooked up that way, installing an aftermarket head unit also won't affect the sub either way.

The remaining question is whether you can figure out a way to repair the appearance of your existing sub or if you want to spring for a whole new one to put in its place. There have been quite a few threads on here where folks have done one or the other approach. If you do a search you can read up on them.

 

 

Slightly off topic, but if you install steering wheel control buttons from a newer model, you can use an adapter and control the bluetooth calls from your steering wheel, as well as the regular volume/channel buttons.

I'd say number 3 is off the table as somebody modified the subwoofer and I doubt the stock amp is even inside of there any more. You can see in your picture where audio connectors were added (round panel towards the back seat) to connect an output from an aftermarket amplifier to your modified subwoofer.

I don't recall the stock sub doing much for the sound, so I'd likely opt for option #1 and gain the extra storage space back there. Ordering the parts from overseas can definitely save some costs.

 

You're right on target actually. We ordered the two steering controls to replace the single. The goal being that a teenage driver needs BT handsfree to avoid distracted driving and a backup camera as well.

The subwoofer is just a nagging issue I need to attend to before we get a new radio installed.

 

Check out Amayama for parts if you opt for option 1.

Toyota 62596-35010-B0 (6259635010B0) TRAY, QUARTER TRIM POCKET
Toyota 62627-35010-B0 (6262735010B0) COVER, SIDE TRIM, RH
Toyota 62594-35030-B0 (6259435030B0) POCKET, QUARTER TRIM, RH
x2 Toyota 64267-35020-B0 (6426735020B0) HOOK, PACKAGE HOLDER NET
I didn't see any results for the two bolts, but you can find them locally if needed for cheap: 90159-A0039

 

What is your location? I have an OEM subwoofer in good working condition that is sitting in my garage. Let me know.

As for replacing it, there are options.

OEM subwoofer- $30 drop in upgrade

Greetings all. I've been doing some recent upgrades to the audio in my 2007 FJ. My goal was to get all the modern features I needed, and improve the overall listening experience in the cabin. I had no desire for a competition audio setup, just something that sounds really good when I'm...

www.fjcruiserforums.com

https://www.fjcruiserforums.com/threads/best-replacement-for-oem-sub.622537/?post_id=8237297#post-8237297

 

What is your location? I have an OEM subwoofer in good working condition that is sitting in my garage. Let me know.

As for replacing it, there are options.

OEM subwoofer- $30 drop in upgrade

Greetings all. I've been doing some recent upgrades to the audio in my 2007 FJ. My goal was to get all the modern features I needed, and improve the overall listening experience in the cabin. I had no desire for a competition audio setup, just something that sounds really good when I'm...

www.fjcruiserforums.com

https://www.fjcruiserforums.com/threads/best-replacement-for-oem-sub.622537/?post_id=8237297#post-8237297

I'm in Western Wisco near the Twin Cities. Please send me a PM, we might be able to put together a deal on that OEM sub if you have the amp with it.

 

I've opted to buy @FJQueue 's non-JBL 2008 TTE sub. (same TTE as my daughter's) It seems like the least expensive and most original way to put this vehicle together for my daughter. I assume the amp is built into the sub and that its straightforward to pull the radio and replace it with a Sony like I did on my non-sub 2014 FJ?