CCRM

When I was having issues with my ccrm (on a 3.8 sn95) I noticed several prongs missing, but that was quite normal as the ccrm didn’t have provision for them they would have been unused, I suspect yours are missing for the same reason
Bill

Fox body cars do not have a CCRM.

They have an IRCM, which is a little different.

Missing pins-that could be normal. All the IRCM is, is a PCB with several relays on it....EEC relay, a/c relay, fan relay, etc. Some cars used the same exact IRCM "box" (housing) and connector, but some had HEDF (high speed fan), or EDF only (low speed fan only and no high speed fan), that sort of thing. Thus, some of the IRCM's do not have the relay-and the pin-for that particular feature, so it will be missing from the connector.

If you suspect that maybe a pin or two is broken, look inside the male connector (harness end) with a magnifying glass. Also look closely at the IRCM's pins; down inside the connector. You may spot one that's broken off. Or better yet take the box apart. On the 4 corners there are some little brads that have holes in the centers. You can drill those out and separate the IRCM box, such that you can see inside of it.