I have a 96 Sport 3.9 V-6 with a manual 5 speed and it runs rough at highway speeds. My problem is mainly in 5th gear at speeds from 50 to 74 mph. When I hit these speeds my truck runs like it is still cold, really rough. But once I get to 75 mph it runs fine. Also in 3rd gear at above 2000 rpm is runs like it is cold too. I've changed the Dist. cap, rotor, spark plugs and wires. Also, I am not getting the check engine light at all.

 

there could be a couple of things, like a bad TPS, MAP sensor, etc. but with pre-OBD II vehicles, the sensor usually has to fail completely before the light comes on. What type of fuel are you using? Also, is the area you live use ethanol? I can't tell you how many times I see vehicles with driveability problems because of ethanol in the fuel. I would try using a fuel additive, the best I've found is Lucas fuel treatment. Pour that in your tank and see what happens.

 

I would suspect electrical, given the info. Like a poor conductive wire, a crossed wire (look for white/grey) or a cracked spark plug. Just because its new, unfortunately, doesn't mean it works these days. When your at 75 mph, are you under load or cruising when it runs fine? Next, I would suspect a vacuum leak or a failing injector.

 

The problem was happening before I cahnged the plugs, wires, dist and rotor. There is also a loud whistle I hear at the same highway speeds. The whistle is not heard at any other time. If I let off the gas, the whistle stops, but then comes back when I level the speed out. If I romp on the gas the nosie goes away. It's mainly when I keep my foot at a constant pressure. I'm in California and currently using the cheap "Quick Stop" 87 octane gas.

 

When I'm at highway speeds, I am just cruising, not hauling or pully anything.

 

The whistle most likely the IAC (Idle Air Control). But that doesn't mean its bad just doing a high adjustment. Sometimes a vacuum leak or something else is causing it to adjust like that.