The only way you're going to get more bottom end than what you've got is to fix what's wrong, tweak the timing a bit perhaps and reduce weight. While the 7M-GE may be stronger than the 5M (or possibly 6M) that your MKII had, the car itself is a LOT heavier.
Check for stored error codes first:
http://www.cygnusx1.net/Supra/TechTi...ror_codes.aspx
If the car feels like a slug until you hit around 4KRPM you should pay extra attention to the vacuum tubing around and under the intake plenum. There's a vacuum actuator down below the Y pipe which controls a butterfly valve in the upper plenum. This modulates the airflow shifting the velocity and pressure. If it is not operating properly you'll see a big loss in power prior to 4KRPM. A simple way to check it is to look at the actuator's armature and rev the engine quickly to over 4K. The system is called the ACIS in the MKIV service manuals (there's a different name that was used in the MKIII literature, but everyone refers to it as the ACIS).
Getting the air filter out of the engine bay is a big priority in my book. Either add some piping and extend it up under the headlight or build a box around it so it's not drawing air from the engine bay... also, K&N filter suck.... I'd replace it with either an Apex'i or a AEM Dryflow filter.