96 3000gt Base NA restore and fix project issues

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Hi,
I just acquired a 96 3000gt Base model (NA) with an Automatic Transmission that has been sitting for an indeterminate amount of time (the tags are still good for another 4 months, but we all know that doesn't mean anything).

Here I will list the issues, and symptoms she has, and the things I've done. Any advice on what to do next is REALLY appreciated.

Symptoms:
1. Bogs out when revved (in park) **Can be revved to 6k RPM, but has to be babied to get there. Full throttle from idle lags out really bad**
2. No power when in gear **Can be babied up to around 30mph, but takes a while to get there, and really touchy**
3. Interior lights, windows, and radio do not work when ignition is on accessory or turned to the on position (they do work when started and idling)
4. Interior lights, windows, and radio do not work when engine is revved up (past 1500RPM)

Known Issues:
1. Bad Fuel Filter (previous owner said he changed the fuel pump, but DID NOT change the filter) Replaced Filter **Worried that clogged filter might have killed the new fuel pump**
2. Alternator charging out of range **Hoping to order new Alternator this coming weekend**
3. Catalytic converter (Temperatures in front and behind Cat have major disparity) **Hoping to order new "Test Pipe" this weekend, to delete the Cat altogether.

Things I've done:
1. Replaced fuel in tank with fresh
2. Flushed fuel lines
3. Replaced Fuel Filter


Next things on list:
1. Replace Alternator
2. Replace Cat with "test pipe"
3. Replace plugs and wires (previous owner said he already did, but I do not trust that)
4. Replace Oil Pump **120k Service**
5. Replace Water Pump **120k Service**
6. Replace Timing Belt **120k Service**
7. Replace Tensioner & Pulley **120k Service**

Any advice yall?