Dan,
You are correct, was once a LAMPS guy. Deck clearance issue sounds remotely familiar, but original mods (I think designated "FLIR CONTINGENCY KIT/FCK, or maybe it was the "Rapid Deployment Kit/RDK" -which it WASN'T) had it mounted ball-down on the stbd stub wing, with wiring through the hell hole. Just more config nightmares as NAVAIR and the HSL Wings couldn't make up their minds on how to do things the right way the first time.
So how's the S fly with the stub wings and stores on? I'm guessing it's somewhat of a pig due to the extra weight and loss of power because of the infrared supression system, unless the -401Cs and tranny have been upgraded. Just my humble opinion, but I'm betting that we'll soon be seeing inexperienced pilots spinning them off the back of the boat, just like they did when Kaman upped the weight of the SH2F without a powerplant or tranny upgrade (that should show you how long I flew LAMPS!)