Your tires are about 3" larger than stock, so regearing the axles a little lower will help greatly. If you're at 3.07 in the axles, consider a set of stock 4banger axles with 3.73 or 4.10 gears, cheapest and easiest route to go.
Replacing the stock airbox and airtube with a performance airtube and conical filter will help quite a bit.
Consider a Firepower ignition kit from
4.0 Firepower Ignition Kit and open the plug gap up to .065".
Then there's performance camshafts and possibly a valvespring change,
Hesco Inc. - High Performance Engine Service is a good source.
I have 62mm performance throttle bodies available if you're interested, they flow a lot more than the stock 55mm. In addition, the taper below the throttle plate found in stock throttle bodies is removed which greatly improves throttle response off the line. Only $95 plus a refundable core charge. Email me at bountyhunter AT sija.org if you're interested.
Exhaust header wouldn't hurt, as well as having the head ported and polished.
Once you start tinkering with the power you can consider a wide-band o2 sensor to keep track of the air/fuel ratio, and google 'adjustable map sensor' so you can tinker with the ratio to compensate for the mods and get the most gains.
Happy tuning.