Duraga, if the new aftercooler was of the right type (and new) and made no difference to the IMT, I suggest you check your system flow rate, and temperature differences over the aftercooler (air and water side) and over the cooling tower. Check at full load (I trust the engine is not exceeding its rating, and is otherwise performing well?).
The pump could be functioning perfectly, but if there's a blockage in the system, there'll be inadequate flow to cool your heat exchanger. Similarly, if either heat exchanger (aftercooler or cooling tower) is furred up, the heat transfer won't be sufficient to cool the charge air.
With no further information, this problem is impossible to diagnose further, and can cause catastrophic engine failure. I've seen a good number of gas engines scrapped by piston seizure because a clogged secondary heat exchanger put inlet manifold temperatures high enough to put the engine into severe detonation.