It does look like it's received some TLC! Stock, non-EGR. No visible leaks up top. How old is the battery?
You said you replaced the
plugs, right, Motorcraft Iridium? I didn't know they had Iridium plugs for this vintage SHO (they do for the Gen 4s)? I believe this is the current replacement for the original plugs -
MOTORCRAFT SP432 {#AGSF32FM, AWSF32F, AWSF32PP} Finewire Platinum Gap: .044"
Did you check/set the gap (0.044 is listed standard, but may vary on the actual plugs)? The SHO is very picky about plug specs. An alternative plug is the Autolite XP3924 Iridium (rebate on it right now makes it cheap), or the Autolite APP3924 Double Platinum. Supposedly even better than the Motorcraft part in performance/longevity.
Did you notice any oil in any of the plug wells?
Can't really see the condition of the DIS and the ground wire that leads from the passenger rear of the intake to the firewall. Can't see the camshaft seal area (oil leak), you will need to put some light on it for pics. Can you get closeups please? The DIS
appears to be fine, just dblchecking.
Hopefully the air filter cleaning/MAF cleaning will work wonders. In any case, would be worth it to pick a standard paper filter (Motorcraft if at all possible, but def a good brand), clean the MAF sensor, go from there, just to have a basis for comparison. Then check the TPS voltage.