I was going to ask about the extra wires that would be with the new head unit.
There could be 3 or more 'switch wires' one sends a signal to an amplifier that causes it to turn on.
Another signals an automatic antennae.
And a third would receive a signal that dims the radio light when headlights are turned on.
These wires need to be capped off securely because they are energized. Can cause a fuse to blow if they contact ground..

.. The poor FM reception has me stumped because it was the same way with the stock radio unit.. Has to be in the antennae.

Try this, turn on the radio to station that you should have good reception to. Then remove/unscrew the antennae from fender of jeep. Did the reception get worse? Or no change?
The antennae should unscrew with little effort, use a wrench to get it started.

By chance do you get good FM reception with the engine off?

 

I think it's the antennae too. He capped off those wires. Let me try your suggestion, be right back...

 

My reasoning is, the reception should get worse after unscrewing the metal antenna. If no change then the signal is being lost somewhere in the cable.

 

No difference, with or without the antennae

 

I'm not sure where the ground is located for the antenna cable. But member Firestorm500 had it right in his post, maybe he knows.
The cable may need to be replaced or has become disconnected from the antenna mount.
You can see if its connected by opening the passenger door and looking behind the hinges with a flashlight. Follow it into cab and examine it.

 

What color is the cable behind the hinge of the passenger door or will I only see that one cable?

 

The antenna cable is black 1/4" diameter, looks exactly like cable for TV. Known as 'coaxial'.
I was examining my antenna routing and found what 'could' be the issue. For the poor reception and the blown fuse.
The cable enters the cab in the passenger footwell. Remove the kickpanel in footwell. Check this connection in picture. Also keep an eye out for any damage to the cable.

 

If antenna cables plugged in at back of radio this is the next place to look. You still have the factory antenna ?

 

Yes, i still have the factory antenna.

 

Ok, but I just had a party for my 6 year old, I was managing 11 kids in a waterpark. Half of them couldn't swim. I'm pooped.

 

Dont ya just love it when other parents drop off there kids and expect free baby sitting service ...

 

All the parents stayed! Even the fathers!

 

So I replaced my #2 and #9 fuses. Radio worked, but shut off and restarted when I hit a bump. Tried to plug in a new phone charger, and the radio shut off and hasn't come back on even after replacing the fuses.