As mentioned above, the ECU, especially the pre '89s are not the best for mods.
With all the money you put into that truck, did you install a new cat or maybe remove it? Any big dings in the exhaust system? A restricted exhaust will limit your RPM, especially under load.
Another thing to check is the fuel pressure/flow. As the engine load goes up so does the fuel need. Under a light load, running around town in lower gears you can spin the engine to the higher RPM levels, but when you get on the highway in high gear with the aero resistance you can max out the fuel system pretty quickly. Then the fuel filter can be a problem here as well.
How does the power come on? Good bottom end torque with nothing on top? Could be the cam is advanced. No bottom end torque with power coming on hard on the top end? Cam retarded. Either way the powerband would be narrow and peaky. Cam could have jumped a tooth.
Ignition timing could be off. Too far either way can kill the top end. When setting the timing do you short the diagnostic plug? Very common mistake when setting timing. Using the old crank pulley/harmonic balancer can be an issue if the outer ring had slipped. Check TDC.
My ['86 4Runner will do 85mph on flat land(uphill is another issue) with pedal to spare. Currently running stock gears and engine with 31s. So I'd say there is an issue to look for.
