Ok, I have looked over wiring diagrams for both the 4T65-E transmission and the 98 Camaro LS1 computer. According to my information, the 4T65-E should work with the LS1 computer, but there might be a few issues.
The 4T65-E has a trans range pressure switch that appears to be identical in function to the 4L60-E's. The exception is the 4T65-E has a pressure switch for TCC release and the LS1 computer does not this. No big deal.
The LS1 computer does have an output for a 3-2 downshift solenoid that the 4T65-E does not have. You will need to "pacify" the LS1 PCM into thinking there is a 3-2 sol by using the appropriate ballast resistor to simulate the electrical load of a solenoid.
The 4T65-E also has an Input Speed Sensor that will not be used by the LS1 computer. However, I believe the 4T65-E has a 29-31 tooth reluctor wheel for the VSS/output speed sensor. This sensor will register about 30 pulses per wheel revolution or about 22,000 pulses per mile for the standard size tire. The LS1 computer is going to be looking for a 40 tooth reluctor wheel mounted on the driveshaft which, with a rear axle ratio of 3.23, this would give the PCM about 130 pulses per wheel resolution or about 95,000 pulses per mile using the standard size tire. So as you can see, these two speed signals differ greatly. However, the LS1 computer should have tables that address the speedo and VSS sensor calibration so this should not be an issue. Other than that, I see no reason why the LS1 computer could not run the 4T65-E trans. In fact, it looks like this will be easier to do than what I am trying with Mr. Pat's LT1/4T60-E combo because the 4T60-E does NOT have a gear pressure switch.
In any event, I will let you know how this turns out for Mr. Pat.