1995 Mitsubishi Montero Strange timing order

I recently purchased a 95 Mitsubishi Montero 3.0 distributorless that was running rather rough.

I decieded to fix a valve cover leak and change the plugs at the same time since they are so hard to get to.

I noticed when I removed the plug wires that number 1 and 3 were out of order and I thought this might have been part of the problem.

The plugs were shot, it looked like the driver's side plugs had never been changed, gap around .065.

I put the plug wires back in the proper order and it ran like crap.

I changed 1 and 3 back around and besides for being cold blooded when I first start it for the day it runs great.

This is what the order should be from left to right according to my Chilton's;

2,5,4,3,6,1

This is what I am running;

2,5,4,1,6,3

This doesn't make any sense to me, I had figured that maybe the coil pack wires got switched around and that maybe 2 and 4 needed to be switched also since they are the sister plugs for 1 and 3 on the coil packs.

I tried that and it ran worse.

Any idea why this would happen?

Thanks

Bret