Need help with my glowplug wiring.Long Thread. Need HELP

[MAS1866]

I've been having trouble with my old man's 2002 F250. 7.3PS 4by auto. He wass having some starting issues and the truck is severely miled up(but runs great when it's running). He replaced the batteries, starter, glow plug and MIAH relays. After he finished all of this, the truck wouldn't start. Oil pressure is good, Fuel pressure is good. So I put my scanner on it and had no communication with the pcm. After some wire checkin' I replaced the pcm. Great, truck starts now. HOWEVER......the new glow plug relay's post were 90* off of the oem relay. The way he had it hooked up was backward(after I bench tested the relay), but the batteries would charge. When I hooked it up the proper way so the relay worked, the batteries aren't charging. Anyone heard of this? So my biggest difficulty is, the wiring schematic in my online Mitchell manual has different wiring codes than the actual truck...so I called the Ford dealer and they agreed to send me Ford's wiring schematic and it matches my Mitchell one. The Truck is as follows...
GLOW PLUG RELAY
Large Blk/Org-(30 post) hot power from batteries to glow plug relay.
Brn & Ylw-(87 post) Power to glow p[lugs.
Ylw/lt blu-(87 post) fusable link to ?
Red- (85 post) power from pcm to relay
Org- ( 86 post) return signal to pcm?
[U]MIAH RELAY[U]
Blk/Org-(30 post)-Hot from Battery
Red/Ylw-(87 post)- fusable link to ?
Heavy Red-(87 post) to MIAH
DkPpl-(86 post) return signal to pcm
RED- ( 85 post)power from pcm
This is the way is is hooked up when the batteries won't charge.
When I reverse the red & orange, the battery charges, but the relay don't work.
Can anyone help with this? Even if you go look at your truck and tell me how it's hooked up and what color wire they are so I have and idea if the problem is somewhere else would be appreciated.

[NoRalPh]

OK first, the relay is just a switch. It uses a very small amount of current to switch a very large amount. Being a switch there really IS No "backwards". Doesn't make the slightest bit of difference what wire is on which side...

The system works like this: there is no power from the PCM. The PCM supplies Ground to the coil (sm 85 & 86 terminals) and the Key is what powers that coil (even these can be backwards!)

So, I can't imagine these connections having anything to do with charging...

Here's a pic;