Evan, I was thinking the backseat cell would be some kind of completely sealed system, possibly even involving unmounting the rear canopy and seats and having some kind of separate ventilation built into the metal skin-section replacing the glass. Dry F414 would be a good start... maybe keep the afterburner but relocate it onto the end of the extended tailpipe? (I'm trying to figure out if you can get enough power for a Harrier-style vertical lift, at a usable weight, while still fitting inside existing skin.)
F414-EPE with AB gets us to 26,400# wet (52,800# total), and both it and A-12's F412 are evolved from the F404, so maybe grafting on the F412's larger fan might give some more boost--but would it be enough to take a 60-65,000# aircraft straight up? Or, IF sources are correct that the INS6 version is rated at about 26,977# (120 kN), that gets us a little closer at 53,954#, but I'd still expect some loss from tapping the bypass duct into forward vectoring. Also, could fuselage reinforcement help with the added load from the composite wing?
Also, F414 takes a 35x154 envelope... most Intruder/Prowler kits are cut with a MUCH shorter-than-correct intake, so could that buy some extra length room?
And another idea... could a dedicated station for two rails and a small ECM pod (kind of a hybrid of F-15A as-conceived and F-15SA/SE Stations 1/9) be fitted under each outer wing, and/or a rail on each tip? A Prowler crewdog I consulted on ARC suggested a limit of 500-1000# on each A-6F/EA-6A outboard pylon for reasons of bring-back weight, but if you aren't trapping on a carrier maybe you could get away with more.