motor hesitates on acceleration and at WOT.

I have a 2003 Mercury 40HP 2 stroke with onboard oil injection. (40 ELPTO)

Couple weeks ago when I was out the motor started hesitating when accelerating and at WOT. Kind of like it was starving for fuel.
I figured a fuel pressure problem so I replaced my old removable tank, fuel line, and primer bulb. i also replaced my external fuel/water separating filter.
A quick test after that produced little to no improvement in performance.

Thinking about taking it to a Merc shop for troubleshooting but would like to see if there is anything else obvious that I could check out first.

Hard to troubleshoot myself since I can only run it on the muffs in my backyard. Cannot seem to replicate hesitation while motor is out of the water. (at least from what I can tell)

Need some help on this one.

Brian that sounds like a fuel pump problem. There is a test you can do but it has to be done in the water. While running and it starts to act up, pump the primer bulb. If it seems like it wants to go, rebuild the fuel pump. If that makes no difference at all, add some Sea Foam to the gas, you might get lucky.

+1 on the fuel pump problem. The rebuild kit for my 90hp only cost about $11 and took about 20 minutes to install and it comes with good instructions that are easy to follow. It sounds like you have replaced most of the other possible culprits so I would go ahead replace the gas filter that is actually on the engine as well. While your at it take a look at fuel tank vent and the anti-siphon valve on the tank just to make sure everything is working properly. I bet you just need a new fuel pump bladder. Please let us know what you find.

+1 on the above two posts. IBNFSHN's test for the fuel pump is the easiest test to do for a fuel problem...all you are doing is using the bulb as the fuel pump. It will work well...if the motor picks up or smooths out its the fuel pump.

and like yikes said...its easy and cheap to do a fuel pump...it just has a little bladder in it. USE MERC/MARINER parts for the fuel pump...trust me on this...will cost a bit more...but will be worth it. I've had trouble with sirra/mallory parts on fuel pump rebuilds. Just my opinion.

To emphasize Scrapper's post a little, by all means use Merc parts, especially Mercs. Merc has a TSB out for the square type fuel pumps used on Mercs from about 1990 to 2000 something. Unfortunatelly I didn't save a copy of it and Merc made them take the site down that use to list all the TSBs. I guess they don't want us to know what's wrong with their motors. Anyway, the kit includes new style check valves. It seems ethanol caused the old ones to curl up on the edges and not seal properly. I went thru this recently and it is true. You should be able to get a copy of it from the dealer. Or just spend the $20 for the kit and eliminate that possibility.

I have run into the check valve deal...thats why I ruined a sierra kit. The merc kit I got came with the TSB in the package. There are parts that do not go back into the pump. In some instances you have to enlarge a hole also...not by much...its quite easy...but without the TSB you will not know. Just like IBNFSHN said, its the check valves. If you don't have the bulliten..well, you mess stuff up...lol. I have a copy of it, I kept it. If you need it let me know, pm me a fax number and I'll get it to you asap.

IBNFSHN...I just thought of something...thats probably what happened to my buddies daddies blackmax. I didn't think about it, because the TSB I got didn't mention ethanol...it just gave new instructions. I remember seeing the old checkvalves and they didn't look real good...I put the sierra kit in with the old check valves...as the sierra kit didn't say to replace the old rubber part with just the new plastic...well needless to say she still would surge and not stay running. Put merc kit in....better made by the way....and did what the paper said and poof!! it worked great. That goes for you too...if you need that I'll try to get it faxed to you...or if you just want a copy.

I use sierra and mallory water pumps, thermostats, carb gasket kits,...but pretty well stops there.

CDI electronics.

And most anything else I will try to use OE stuff.

well did have a vent hose off a built in gas tank kept sucking closed

the boat would get enough air to idle just fine in gear. But once on plane the motor would stall out.
But that is not your problem cause you replaced the removable gas tank.

but thought i would throw that in. for anyone else having problems.

i had a scratched cylinder on a motor and it was losing compression on the top end, rpms would suddenly drop off

Mine acted like yours, it is much older, but it was not the fuel system. One of the coils was bad. I didn't figure it out till I was working on it after dark. Saw fire jumping and put new coil on. Fixed it right up.