Bad ground, or HU problem???

Installed a Kenwood unit. Used a SWC interface from CRUX, and also retained the JBL amp. Soldered all the wiring, and did NOT use the factory harness for grounding--ran a larger gauge wire (14) and connected to a scraped frame bolt. Because of the tight space behind the radio (went from a single to a double), the power lines and ground lines run fairly close, so I do get a very minor alternator whine. Here's the issue. On initial startup of the radio, it sounds great. After 15-20 minutes, i get the occasional "snap-crackle-pop" through the speakers....initially, just one or two every 5-10 seconds. After that, they become more frequent. WTF? If I shut the radio down for a period of time, it's the same thing all over again. Sounds good at first and then the popping starts again. HU problem? Grounding problem? SWC/JBL interface problem? Somebody hep a brotha out....I'm losing sleep over this......