As far as changing the bulbs to LED's and causing EMI in the radio, I'm not so sure that's the whole reason.
Adding in the HID's and getting some EMI through the radio is feasible. Where are your ballasts located? Depending on how long the wires are, some people mount the ballasts up by the "firewall". Not exactly ideal. The HID's take >5000 volts to start the arc, and some setups even maintain that high of voltage. That creates a lot of electromagnetic waves around the wires going to the bulb. Those waves induce voltage in surrounding wires, and can result in your issue. This is the same reason why DOT approved spark plug wires are high impedance(they transfer up to 60,000volts), otherwise you get some really weird shit going on.
Back to the OP though. If all you did was remove the light bulb "tray", install the LED's and reinstall them, I don't see how that could cause the issue. Unless there was an issue in the first place and somehow by moving the wires and such around, you discovered it.
Make sure all the wiring is connected properly, and IIRC you should have the amp mounted in the rear as well. Double check the connection at the amp as well.
Have you tried putting the bulbs back in to see if the noise goes away?
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