Fixed wire on fuel pump now car runs terrible.

What sized fuel pump do you run?

Sometimes crappy running motors are a result of a bad MAF.

Dump the codes and see what the computer says is wrong…

Here's the link to dump the computer codes with only a jumper wire or paper clip and the check engine light, or test light or voltmeter. I’ve used it for years, and it works great.

See http://www.troublecodes.net/Ford/
OR
See http://www.mustangworks.com/articles/electronics/eec-iv_codes.html

IF your car is an 86-88 stang, you'll have to use the test lamp or voltmeter method. There is no functional check engine light on the 86-88's except possibly the Cali Mass Air cars.

Codes have different answers if the engine is running from the answers that it has when the engine isn't running. It helps a lot to know if you had the engine running when you ran the test.

Trouble codes are either 2 digit or 3 digit, there are no cars that use both 2 digit codes and 3 digit codes.

For those who are intimidated by all the wires & connections, see http://www.actron.com/product_detail.php?pid=16153 for what a typical hand scanner looks like. Normal retail price is about $30 or so at AutoZone or Walmart.

Or for a nicer scanner see http://www.midwayautosupply.com/detailedproductdescription.asp?3829 – It has a 3 digit LCD display so that you don’t have to count flashes or beeps.. Cost is $35.

I don't know if you can put a fuel filter in backwards, but you might look into that...although it does say pretty obviously which directly it's supposed to go.

Are you sure your wires are connected securely?

There's a possibility that it could be low fuel pressure...do you know what your fuel pressure is? Idle fuel pressure might not be as good as fuel pressure when you hit boost since that's when your problem occurs, so that could be a problem if you don't have an in car fuel pressure gauge. I'd see what the other guys think, though.

So it's fine outside of boost, but once you hit boost, you notice it?

A latched EEC relay can keep engine management circuits full of juice when the key is off (not sure if that could be happening here - I did not really follow what is happening. Just info).

Good luck.