Tons of stuff.
Air Cleaner: Try getting a blower hat for a carb from a Vortec or Paxton kit and build some 3-4" intake tubing down to a cone filter. Install the IAT sensor as close to the filter as possible, sheild the filter from engine heat and out side water intrusion. A good welding shop can tig weld one up really nicely, you'd just have to cut and fit the tubing to match. Some nice turbo hoses can clean up the install at the joints. This will give hood clearance, see the intake section.
TBI: Holley p/n: 502-9 for '90-'95 TBI engines. 2" throttle body bores, 670 cfm, 79 lbs/hr injectors.
TB spacer (to intake) JEG'S p/n: 555-15401.
Injector spacer JEG'S p/n: 555-15410.
Fuel Pressure: GM compatable adjustable regulator. Adjust upto 16psi as needed. Get a new in-tank fuel pump.
Intake: Edelbrock TBI p/n: 3713 *TB bores will need to be enlarged to 2" dia for Holley TBI unit, no mods needed for OE TBI*
-Holley sells a TBI intake that fits 2" bores p/n: 300-66.
-GMPP p/n: 1249681 fits Vortec and Edelbrock E-tec heads. *requires TB bores to be enlarged for Holley TB, remote EGR tube from exhaust manifold to intake.
***Check hood clearance before buying***
Stock style (may require inner 2 intake bolt hole mods, very minor): GMPP L98 heads p/n: 12556463, WP Sportsman II 200 p/n: 011150-1, Edelbrock p/n: 60859.
GM Vortec style (requires GMPP intake, EGR mods): GMPP stock vortec p/n: 25534421, hipo 12558060, Fast Burn 12497186, Edelbrock E-tec p/n:60979/60989.
Cam: Factory hydraulic roller, GEN I OE roller style. Tons of options here.
Short-Block: generally they have a nodular iron crank, powdered metal rods, and hypereutectic pistons. A good base, even though they are only a 2-bolt main block.
Exhaust: Impala SS manifolds or aftermarket headers. Edelbrock 66032/66033, Headman 68700/68706 (may need welding to fit).
Get a dual exhaust cross member from a '94-96 B-car.
Dual pipes are available from Dynomax p/n: 17375, Flowmaster p/n: 17118K, JEG'S 555-30410, Edelbrock 5670, OE dual pipes are available from NAPA (Tenneco Automotive bends them) but are special order.
Transmission: Upgrade the 4L60E with a shift improver kit B&M p/n: 70360; HD 2/4 gear servo TCI p/n: 376006; Governor recalibration kit (upshifts) B&M p/n: 20248; TV kickdown valve (more speed in o/d) B&M p/n: 70237.
Rear End: Your wagon has a 8.5" 10-bolt with 30 spline axles. Probably has 2.93 or 3.08 gears. I'd upgrade to 3.42s as a minimum, but I'd prefer 3.73 or 3.90s with stock 225/75/15 tires.
3.42 GM p/n unk, and Richmond p/n: 49-02781, 3.73 GM p/n unk, and Richmond p/n: 49-0041-1, 3.90 Richmond p/n: 49-0034-1.
All gears fit 2.73 and up carier.
Limited slip units: Auburn p/n: 542022, HD Auburn p/n: 542052.
I hope that helps, PM me if you'd like.