Your 3.5 can have the cam replaced and possibly even hi comp pistons fitted without even removing the engine from the vehicle. The 3.9 is worth about 10% extra torque but the 3.5 modded will produce same power or better at the higher end of the rev range. And it will last longer.
Also if your power is down have the distributor mechanical advance checked/recurved and run the idle timing at 6 to 10 degrees BTDC.

