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There really are no simple upgrades for the 7M-GE which net any notable power increase. Leave the intake alone and get a good fabric filter element for it (Toyota or possibly a K&N). A good one piece drive shaft will reduce the rotating mass and friction losses incurred by the incredibly heavy two piece driveshaft. Making sure the car is operating at 100%. Make sure you have the right spark plugs in, a new rotor and cap, New spark plug wires run the right octane for your driving and environment (premium isn't always best... less kinetic energy). Generally go through the FAQ section VERY thoroughly but disregard anything turbo related as somethings are not the same for naturally aspirated engines (such as running extremely large intakes and/or exhausts).

There is no way to shorten the intake enough to see any benefit and short ram intakes and much like short runners it'll negatively impact intake velocities at low loads. The 7M-GE uses modulated intake system to switch between long and short runner modes, make sure this is operating properly and call it a day. Leave the Helmholtz resonator in place too.... despite gear head cooler talk it has been well proven that it helps and if you look at it closely only and idiot would believe that it's a restriction.

Reducing the car's weight is really the biggest thing you can do but to seriously reduce the weight is a long and tiresome task.

Personally, I'd just focus on cleaning it up as much as possible and save any other money for buying a Turbo model later on.