May want to double check that there is good grounding on bare metal so that the amp discharges into ground and not the woofers...also, most decent amps have internal soft power up/down features that prevent popping. I'm not very familiar with the shaker H/U but most aftermarkets have an integrated time delay on the RTO that allows the amp to power down before the radio.
Is this amp on the OEM woofer's?? or for those CDT's?? The OEM woofers are an odd 1.2ohm load...either way I'd see what this audio shop plans to do for you...that would be a PIA