Rough Idle - Injector Issue?

Our boat is a 2007 Sanger V230 w/5.7 'black scorpion' engine. It only has 169 hours on it and it's running pretty rough.

Last the boat started idling poorly and would die when you put it into neutral. I found that emptying the fuel/water separator helped the problem temporarily but that never lasted more then a couple of engine hours. Nearly every time we used the boat I was emptying the fuel/water separator. At the end of last season I drained the fuel tank, filled with fresh gas, and it was running almost back to normal (say 95% normal). On the last trip out to the lake I ran the boat out of gas. Luckily it died right as I was pulling up to the gas dock so it didn't ruin the day. Once I filled up with gas, the boat was back to idling like crap.

Fast forward to this spring, I take the boat to our mechanic and he checks it over, scans the engine for codes, empties the fuel/water separator (no water in it), and changes the spark plugs because they were fouled. He ran the boat for a minute on a fake-a-lake and the rough idle was gone. He said to put some time on the clock and if the problem came back then we most likely needed to have the injectors pulled and cleaned/rebuilt because the water in the gas last season likely clogged them. I'm not really mechanical so I have no idea if this is a common issue or problem? For a boat with such low hours I wouldn't expect to have to an injector issue, but I really don't know...

Pulling the injectors and having them cleaned/rebuilt will cost a pretty penny and I don't want to spend that money if I don't have to. Does anyone have any suggestions or thoughts on what our problem(s) may be and to fix it?

btw - I have no idea where the bad batch of gas came from (assuming that's our problem). We treat our tank every winter when we put it away.