I have a 66 F-100 stepside, 2 wheel drive shortbed. I am considering putting in a ford lighting motor (out of a wrecked 2003) with transmission. Or building a big block that I have sitting in storage to put into the truck.

The question is does anybody make an aftermarket wiring harness, will I need one, and will the motor fit under the hood with the supercharger on it. The lightning was rear ended and totaled, but all the stuff under the hood was not damaged.

 

That will not be an easy job. My usual response to people, and I'm not trying to be a smart-aleck, is that if you have to ask the question then you probably aren't qualified to do the work. A swap of that magnitude is NOT going to be plug-n-play.
I'll assume the Lightning frame is toast. Would have been almost easier to move the body to the Lightning frame, though that still is a lot of fab work o make it fit (especially if your truck isn't a short bed!).
Anything can be done if you have the time/money/talent.
I believe the Lightning engine does actually fit under the Slick hood. I came across a guy who built a Slick Lightning...he moved everything, including the interior, to his 65-66 truck. I spoke with him at a show for quite awhile and it was a huge amount of work, done by a guy who has a background in custom car fabrication. But it did fit under the hood without a scoop. The FI wiring would have to be pulled from the Lightning intact and grafted into your truck. The fuel tank would require a return line which it doesn't currently have. And of course, you'd have to address the undercarriage of the truck as there is NO WAY I'd ride in a Lightning powered Slick 60 truck with stock brakes and suspension.

 

Sounds like I'm gonna go with the big block......thanks

 

There are some intakes on the market and due out very soon for fuel injection setup for the FE. Try the forum for more details...I'm a stock guy myself.. ok with a little bit'o pep but no aftermarket crap.