My bike has been built from 4 different motorcycles, Harley, GSXR, Ducati, and newer GS parts. All the wires have been rerouted and ignition under the seat. I havent changed a thing and its been riding great for over a year. I laid it down a couple weeks ago in the rain, not much damage was concurred. I started working on it today and cranked it and let it run. I never have had the seat off when it is running but this time i did and I examined all the wires underneath the seat to make sure everything was in it place and while doing that I noticed the wires and boxes were extremely hot! Is that normal?

Extremely hot is VERY abnormal for any electrical system....heat & wiring don't mix.
Were u continually trying to crank it over?

That is what i was thinking too. No it cranked right up. Nothing was smoking or melting concerning the wires but probably wasnt far from it. It ran maybe 8 minutes.

I can only generalize cos i don't know the setup with your hybrid.
When wiring gets hot it's often caused by excessive current being draw for that particular purpose....either that or the guage wire is below standard to start with.
If the PO has replaced wires that are getting excessively hot i would consider replacing his replacements.
Convince yourself first that nothing is shorting-out & everything BUT the wiring is fine.

Heated wires are either absorbed heat from something else close, too many amps being drawn or bad/loose grounds. Could also be a sign of a component dying

Ok, I am using the original wiring harness, no extra wire has been added or anything to create more drawing of current or power. Ill go through it and check for a short. Something may be grounding itself out.