sounds like your speakers aren't connected properly. check your speaker leads coming from your radio and make sure they are positive to positive and negative to negative. if you're using an external amplifier,check your RCA cables and your speaker outputs on the amp. make sure thr remote turn on lead is connected, otherwise the amp won't even power on.hope that helped, good luck
The PCM is programed for the LS engine parameters and now that you have changed engines the signal from the new engine are out of parameters> Either see if you can get the PCM reprogrammed at a dealership or purchase a new PCM and program the chip with the police engine interceptor to the vehicle> you may also return to the place where you got the engine and purchase the PCM for the police vehicle.
Sounds like a cracked intake manifold crossover tube. Very common on the 4.6 liter. The new intake has been updated with an aluminum crossover. I’m happy to assist further over the phone at https://www.6ya.com/expert/jeremy_d728a59f986299fa