I didn't butcher anything, I bought the adapter that goes from the factory harness to jvc hu. This has Jacks that plug behind the jvc for the factory speakers. I don't think I would but do I need to buy those adapters for both antennas or can I just use the big one? The amp thing is confusing me, what do I need to do with that, is this not allowing me to get sound.
To answer your question about the antenna plug, yes you can just use the big one and leave the little one unplugged. Some people get those adapters to bridge both antennas but it's not necessary. I didn't use the adapters on mine and only used the big plug for antenna directly into the head unit and my reception is fine.
Additionally, on my brother-in-law's 4runner, his main antenna was broken so we got the adapter and only used the small antenna jack (the one for the antenna built into the rear window) and even that netted him decent reception. He said he didn't care about FM anyway.
If you search this, some people say bridging the two antennas is a good idea, others say it's not. The factory radio is designed to use one antenna or the other depending on signal conditions, but I don't believe it used both at the same time. This is what I gathered from my research doing the same install.
What everyone is suggesting you do is to bypass the factory amp and use the amp built into your head unit. To do this, you need to connect the harness from your head unit to the vehicle wiring BEFORE it reaches the factory amp. This is why you need to look below the factory head unit, find the amp, and find the connection from the back of the amp out to the speakers. This is where you plug in the adapter harness if you got one. I used this:
http://www.amazon.com/Metra-70-1761-Wiring-Harness-Speaker/dp/B0002BEQJ8/ref=sr_1_1?ie=UTF8&qid=1458485202&sr=8-1&keywords=toyota+harness+metra
You need to wire that harness into the one that came with your head unit. Then you'll have a harness which on one end plugs into your JVC head unit and on the other end plugs into the vehicle's wiring (the vehicle end of the harness plugs in at two different places I believe). Also, make sure your using the amplified outputs from your JVC and not the red/white RCA plugs which are not amplified.
Now if your trying to keep and use the factory amp with your aftermarket head unit, I can't help you there. Not sure how or if that would work.