I agree with MikeB. The guide plates are not aligned and causing the rockers to not contact the stems properly. The solution is either correct the geometry with these heads or replace them. You might be able to utilize offset rockers but that isn't common.
The pan should not be an issue unless it is bent. The depth of the pan is determined by the clearance issue of the vehicle. The block should be milled for clearance of the rods and that is a known issue with the build you are doing.
I used the factory harness from the wiper switch to the pulse module and the painless harness from the module to the wiper motor. The connections on the module for the painless wires I used are B-pink 963
C-purple 964
D-ground...
There is not a plug on the market to plug up to the harness. You can purcahse plg bodies and build your own, which I would recommend. The idea of unplugging all those wires one at a time is enough to make you want to drive a Ford.
I bought mine from LMC and it fit great. I did buy the crew cab carpet but my truck isn't a crew cab; I used the extra carpet to cover the back of the cab since I have buckect seats in it.
Which Painless harness do you have? Is it the universal or the truck specific?
I just finished installing one on my truck that was specific and can give you the wire numbers if you have the same one.
89Suburban they make cats for headers that will pass in most states.
Guess I am the odd ball on this subject, but I prefer the Pypes Street Pro mufflers.