01 ford explorer subwoofer thump when starting

I recently installed an aftermarket stereo with the help of some people from this site, so I'm hoping to get some more advice. After purchasing the wrong wiring harness, I was able to install my new radio and still use the factory amp and sub, but now when I start the car the sub makes a loud thump. I've read its too much power coming from the radio, but what do I do?

I had that thump too when running the factory amp. It's the sudden jolt in power to the amp as it turns on, causing the thump.

Make sure the gain isn't to high (Not adjustable on factory amp, my bad.)
And make sure the remote turn on wire is hooked up correctly.

Honestly, your best bet is to get an aftermarket amp.. the stock one is junk.

Probably the remote turn on connex. I am running an K'wood HU with 4 new Pioneer door speakers with the factory amp and an Excelon shallow mount sub. Sounds excellent with no power on thud. Now, I agree that the factory amp ain't no high end component, but when matched to the appropriate HU and sub it sounds fine. IMO the factory sub is the more crappy component.

Sounds like you have your remote wire attached to your power antenna wire. your antenna wire in an aftermarket head unit usually tells your antenna to retract or detract but it can also turn your amp on and off. Its an easy fix. Or a bad ground

Install this.

http://www.crutchfield.com/S-zBOlXBcmTDB/p_120AFDI5V/Axxess-AFDI-5V.html

Other option is to put a 1.5k ohm resistor in series with the remote line on the amp. Whats happening is the amp uses a 3v remote signal from the factory, and your aftermarket is supplying 5v. The resistor will drop the level to around 3v at the amp and get rid of the pop. Should cost you about a buck at rat shack, or around a penny from newark or digikey.