IMHO 0411 PCM is lightyears ahead of what is inside of any aftermarket EFI system today. This is primarily because of emission standards the manufacturer has to achieve that Holley never cared about.
Might I ask why are you considering this controller swap? There are 2 better ways you can go that will keep your vehicle's controller in place and happily communicating with all of the other vehicle modules.
1 - If you don't want to break open your new motor you can simply buy and install the Lingenfelter TRG-002 module. It is almost plug and play with your cam and crank sensors and then you have to connect ignition power and ground. This box will take in the 58x4x signal and output the 24x1x your gen III PCM is looking for. You can get that box here: Lingenfelter TRG-002 LSX Engine 58X To 24X Trigger Wheel Conv Control Module Kit
2 - alternatively and the correct and proper way to apply a gen IV engine to your gen III car is to open the engine when you get it and swap reluctors on the crank. Put a 24x wheel on the LS3 crankshaft and find you an early LS2 1x camshaft sprocket. Then you only need to extend your camshaft sensor harness to the front of the motor. And yes if you go that way the LS2 silver blade throttle body can be wired right in and the gen III TAC module will play with it just fine.
Also if you do keep the gen III controller you should try to keep the gen III MAP sensor. The LS3 intake has a larger hole and so you will want to replace the grommet on the MAP sensor with a thicker piece of hose so it is a tight fit. The gen IV map is a 1.25bar thing and the gen III controller is only 1 bar or 2 bar or 3 bar pending the OS we apply and so when we wire in the gen IV MAP to the gen III controller the end result is lost tuning resolution in breakpoints you never get to have.
The Holley controller will use a wideband and let you see outside 14:1-15:1 afr but it will only look at 1 bank and has no ability to trim seperately. Holley controllers also lack the factory calibrated knock sensors if we are trying to use those for power tuning. That Terminator X Max is a step up for up to a optispark driven engine controller but I feel like they are only better by that point for their reliability. Again in my opinion.
If you go with the X Max I do not think it matters if you use LS2 or LS3 throttle body. But you will live with warning lights on the dash and systems that don't work. Important systems like anti lock brakes and traction control that require a high speed connection with the engine controller for proper operation. But also the BCM and the vehicle's anti theft system. If the BCM and PCM can not shake hands then you will always have security lights on the dash.
FWIW I ran the TRG-002 box on my C5 for 7 years with the LSX376-B8. It never gave me a problem except a slightly longer cranking time which I attributed to the box needing to see a signal before it can send it out. And for this reason I wished I had opened the motor and just set it up to be a 24x and 1x motor. Which isn't extremely hard to do before the motor goes in the car.
Might I ask why are you considering this controller swap? There are 2 better ways you can go that will keep your vehicle's controller in place and happily communicating with all of the other vehicle modules.
1 - If you don't want to break open your new motor you can simply buy and install the Lingenfelter TRG-002 module. It is almost plug and play with your cam and crank sensors and then you have to connect ignition power and ground. This box will take in the 58x4x signal and output the 24x1x your gen III PCM is looking for. You can get that box here: Lingenfelter TRG-002 LSX Engine 58X To 24X Trigger Wheel Conv Control Module Kit
2 - alternatively and the correct and proper way to apply a gen IV engine to your gen III car is to open the engine when you get it and swap reluctors on the crank. Put a 24x wheel on the LS3 crankshaft and find you an early LS2 1x camshaft sprocket. Then you only need to extend your camshaft sensor harness to the front of the motor. And yes if you go that way the LS2 silver blade throttle body can be wired right in and the gen III TAC module will play with it just fine.
Also if you do keep the gen III controller you should try to keep the gen III MAP sensor. The LS3 intake has a larger hole and so you will want to replace the grommet on the MAP sensor with a thicker piece of hose so it is a tight fit. The gen IV map is a 1.25bar thing and the gen III controller is only 1 bar or 2 bar or 3 bar pending the OS we apply and so when we wire in the gen IV MAP to the gen III controller the end result is lost tuning resolution in breakpoints you never get to have.
The Holley controller will use a wideband and let you see outside 14:1-15:1 afr but it will only look at 1 bank and has no ability to trim seperately. Holley controllers also lack the factory calibrated knock sensors if we are trying to use those for power tuning. That Terminator X Max is a step up for up to a optispark driven engine controller but I feel like they are only better by that point for their reliability. Again in my opinion.
If you go with the X Max I do not think it matters if you use LS2 or LS3 throttle body. But you will live with warning lights on the dash and systems that don't work. Important systems like anti lock brakes and traction control that require a high speed connection with the engine controller for proper operation. But also the BCM and the vehicle's anti theft system. If the BCM and PCM can not shake hands then you will always have security lights on the dash.
FWIW I ran the TRG-002 box on my C5 for 7 years with the LSX376-B8. It never gave me a problem except a slightly longer cranking time which I attributed to the box needing to see a signal before it can send it out. And for this reason I wished I had opened the motor and just set it up to be a 24x and 1x motor. Which isn't extremely hard to do before the motor goes in the car.