Nice!

Did you reprogram the PCM?

Is the bottom end stock?

Is the supercharger pulley the stock size?

How many miles since you started driving it with the supercharger?

The engine block itself and the transmission is still stock. I never did reprogram the PCM I just have boost all the time. Still trying to figure out how to manually be able to bypass boost when the car is idling. The supercharger pulley is stock but the harmonic balancer has a smaller drive for the supercharger belt line.
I supercharged this car with 164,000 miles on it and I’ve almost put 10,000 on it.

This is what it currently looks like.

My son wanted to SC his 5L Mustang and had a kit much like that. It wasn't bad to do but I don't think it'* for someone who is not somewhat proficient with using hand tools
You have a bit of wrenching in you.

Thank you I appreciate that. This model was set up to either be stock or supercharged from the manufacturer so my car was somewhat set up so that I could just switch everything out with parts from a supercharged 3800.

Wow sounds like it'* working well. Maybe the PCM just thinks it is at really low altitude where lots of air comes in.

I never thought of it that way lol

your boost bypass actuator/valve thingy is still on the supercharger and you have it hooked to vacuum. under proper operating conditions, it should be bypassing at idle IIRC. Verify the rod on that actuator is able to move smoothly, you can actuate it when the car is off. there is also a vacuum test with a handheld pump iirc that can determine if its okay. the boost bypass circuit (which a 96 l67 pcm would be able to control Im pretty sure) will force the actuator to bypass when in reverse, traction situations, overboost situations.. etc..
Also I suggest doing some lugs on your battery negative and/or new cables , been there done that it never ends well like that
ALso I WOULD NOT SUGGEST YOU KEEP YOUR FUEL INJECTION LINES CLAMPED WITH WORM CLAMPS. THAT IS A huge SAFETY ISSUE. You can repair the original design with vinyl(meh) or if you insist on the hose, use FUEL INJECTION clamps(sold at auto stores) and fuel injection hose(specifically for FI) and look up the proper hygeine for that. I dont want to see your park avenue end up a crispy corpse

Also for your personal liking, you should upgrade your alternator when possible to an AD series alternator (or a CS130D, same thing but not as reliable long term) which requires a conversion plug from the CS130 you have there.
This tells me your harness was a pre 94 car as well? 94-96(96-98 as well) should have a CS130D and a oval connector on the alternator
Also it appears to be missing a mounting bolt, I hope that alternator has a third connection/mounting ear

Something like this

Also I dont think the air filter is doing as much as you think it does, albeit its prob better than the stock 90s airbox
Getting a constant tension clamp or 2 for your rad hoses (which seem nice/newer) will also be wise so you dont have any leaks over time

My mistake on last post, your alternator appears large. does your car originally have a KG9 or so on the RPO list, which would be a 140 amp charging system? If so, that would be a CS144 and is proper "kind" but it would never hurt to upgrade to a newer kind although may require buying one with a special mounting ear setup

The SC engine has the NA software?

lastly, On your transmission, did you service it properly before the swap so that it was in good health?? (if you had it for a long time) I just ask because Id be worried about blowing up the differential on it because your pushing more boost than a stock 96 ultra and you dont have the 4t60e-HD upgrades to "handle" it lol.