Thanks for the photos. I now see that I just need to move the transmission skid plate forward, so that it covers the front diff. Currently, as it sits, it protrudes to the back of the transmission crossmember and even covers a little of the transfer case (see on the pics I posted above) I just tried to align the holes that where already drilled on the plate with the captive nuts on the provided skid plate cross member, but I guess I need to just drill new holes.
No, your middle skid looks to be in the right place to me. You need a front ASFIR skid to match, or trim the back off a factory splash guard to just overlap it.