Check the voltage on the white wires on the fuse box with the ignition switch off.
It should be 0 volts.
You mentioned clean up, did you remove the fuse box? If yes did you insure the link on the back of the fuse box correctly oriented? The link ties fuse 3 & 4 together. If the box is oriented incorrectly you will have some crazy electrical problems.
Check the items I mentioned and let us know what you find.
Clifton