Theres not much info provided that would help to diagnose/pinpoint the problem. Here are some things that I would want to know:
1) What is the static (at rest) battery voltage at the battery terminals, head-unit, EQ and at the amp terminals. Use both the B+ wire and components GND wires for this test. Putting the voltmeter's GND lead on the battery ground doesnt include that ground circuit and connection at the component.
2) By what means did you determine the amps are in protect-mode, rather then just not powering on
3) If you jump the amp's remote turn-on wire directly to the B+ lug, does the amp power up and stay on. If its indeed going into protect mode and the battery voltage is sufficient, then disconnect all speaker loads from the amp and power it back up. If it comes up without going into protect mode, then there is a short in a speaker circuit.
4) If the amp will power up like it should, then connect an MP3 player right to the amp using a 3.5mm x RCA cable and see if it plays music.
5) I would try to bench test the head-unit connected to a known good battery source and connect a test speaker to each output and see if it plays. Next, test the voltage on the blue remote turn-on output. Should be 12V+. If all look good there, then take it back to the boat to retest, but leave the EQ out for know. Also, you should be able to use the EQ as the source unit with your MP3 connected to its input using the same cable you went directly to the amp. Just keep in mind that your EQ may need to be signaled on its turn-on circuit as if the head-unit was there, and if it doesn't have its own turn-on output, you will need to jump the turn-on at the amp again.
Spending a little time with some test equipment will save both time and money in part swapping. Also, if something is not wired right, any replacement gear you plug up will suffer the same failure. Hope this helps.