Doesn't it log any fault codes in any other ecu relating to comms issues with ipc.

Can you see if there is any common earth for any of the ecu's.

Could be a problem with the cluster connector but i think 2004 is probably a modified type.

I'd suggest to test power/grounds at ipc when it loses comms and test CAN with a scope.

I would refit the original bcm and ipc but use the 2nd hand engine ecu. Reset/regrogram the bcm and ipc as you can pull the security code with op-com for both ecu sets.

You did get the matching transponder chip with the used ecu set didn't you?

thanks
lee