I bought a 2003 Bass Tracker/40HP earlier this summer and it's ran great until yesterday. It started ok, but about 20 mins in, I started getting intermittent power. It would drop down, then return to full power within a few seconds. It did this the whole time I was there. I'm going to start with plugs and hoses I guess, what else should I look at? Thanks

Fuel Filter would be the first thing.  When was the last time it was changed?  Also did it loose power at low rpm's or just on the high end?  If it's just at the high end odds are your engine isn't getting the fuel it requires and the fuel filter would be the first place I'd start.

I don't know when but I'll check it. It was on the high end..thanks.

Yeah, then it sounds like it was starving for fuel which would lead to your loss of power.  If it was constant and missing then it could be the plugs. But I'd change the filter and test it if you can.  

Will do...

OK in the fuel filter there was some orange gunk...not a lot but maybe that's the problem. I've cleaned it all out and will put it back in tonight after work and test. Is there a reason to replace it? Looks clean now.

Replace the filter.  Just  because you cleaned off the "gunk" doesn't mean the filter material is not clogged.

 

My filter gets replaced on an annual basis, whether it needs it or not.  Preventive maintenance is cheaper than curing problems arising from a lack of maintenance.

Your fuel lines may be deteriorating from ethanol

Yeah, I'm concerned about that. The previous owner said he always put in Enthanol treatment. I buy Ethanol free when I can and add treatment as well.

OK in the fuel filter there was some orange gunk...not a lot but maybe that's the problem. I've cleaned it all out and will put it back in tonight after work and test. Is there a reason to replace it? Looks clean now.

Yes I would replace it.  I'd Keep an extra one on hand as well in the boat (vacum packed if possible to keep any moisture out).  If you think your fuel line is bad here's a couple ways to check.  First if you have extra hose you can spare, then cut a small piece off and split it to see.  Also if you bend the fuel line and it shows cracking, then it needs to go. 

My Tracker was doing the same thing and it turned out to be the fuel pump. $30 for a rebuild kit and it was good as new.

 

Brute

My 76 merc was same way. All new fuel lines and good to go. Runs like new.

Also, ethanol is your enemy even with a "treatment". Go ethanol free if at all possible. 

Replacing the fuel filter and both plugs has fixed the issue. One of the two plugs was extremely loose, so I'm sure that wasn't helping. Thanks for the help.