Engine Wants to Cut Off While Running

I drained my fuel cell cup and changed my fuel filter, also added a fuel additive to the gas to clean. I removed the priority start from my main battery. All the electrical work I did was disconnected and still when going about 20 to 30 mph, the engine light will come on and there will be about 2 or 3 hesitations. Appears to be a drop in power but the boat never cuts off. I have also noticed that my engine temp is about 210 even afetr being in the water for 15 minutes. Is that normal and what temp should it be around for a 98 Sport?

A 98 with 36 hours, my first question is how old is the gas?

I have a 98 Sport Nautique that I bought from a owner Harley Davison Dealer back in March 2006. He had it in storage and had only used it about once or twice a year with only 36 Hours on engine.
When I am running the boat, it will appear that all is OK, then suddenly, the engine light will come on and the boats power weakens with 2 or 3 pauses (sounds like it trying to cut off). The temperature gauge, oil pressure and voltage appears OK. I will slow the boat down and its running OK, the engine light will go off after about 10 minutes.
Another problem is when I turn the ignition to start the boat, it won't start, it appears that the battery is dead or weak but the voltage is between 12 and 14 on the guage. I will then have to turn off my blower and the other accessories, and afer a few attempts, it will start up. I then thought that I may be pulling to much amps with my the radio, stereo amp, blower, etc which is causing it not to turn over and the engine pausing problem above. So I did a test, I will run the boat with out any accessories on, and still the engine pausing and it not turning over sometimes appears.

List of things that I have done to this boat recently:
1. Installed 2 tower speakers and added 2 amps (1 for the 4 factory speakers & the other for the 2 tower speakers. I have an inline fuse to each amp along with a switch to power them on/off.
2. Installed a Lightbar for the tower with 3 Lights. I ran these lights directly to the spare accessory swith on the dash. 1 swith operate 1 light facing forward and another swith operating the 2 lights facing backwards.
3. I installed a Priority Start (Battery Protector).
4. (Fix Attempt) When I thought that my single battery was not putting out enough to run my boat with the stereo/amps on, someone suggested that I install a 2nd Battery (Deep Cycle) and run both batteries to a Perko Switch so I can alternate the battery depending if I am running the boat or hanging out in the water. I also ran a + and - terminals. The problem still remains.

(Fix Attempt) Someone on my boat that noticed my problem twice that day, felt like the boat was trying to cut itself off and the Priority Start may be the issue. We took it off the main battery and the boat ran just fine the rest of the day.

So today, I go out to the lake this afternoon and both problem persist. Sorry for being long winded, just wanted to share the details. Can any help!!!!!!!!!!!!!!!!!!