I would suggest you call Whipple and get some guidance. The plugs look reasonable but the soot on the transom says rich and new plugs aren't going to change rich.

I would tell you to check thermostat, but with whipple what is cold start temp set at in program. those are what normally aspirated fail-open t-stat looks like that I worked on.

If this motor is in your "03 you have listed in your avatar. They had a "not so talked about" recall on incorrect pushrods in the mag. motors "mostly". I think mercury put a white paint spot on the back, top side of the heat exchanger to let you know the motor had the new upgraded pushrods. Dont quote me exactly on the color of the paint, But read it somewhere before. Have done a couple just here recently that have broke off the ball on the end of the pushrods and the operator didnt really know they had a problem for a while (months). One had the same symtoms you are talking about. If you do have this DONT buy the merc. pushrods !! Way too expensive you can get them through any auto parts store from speedpro $70 a set. Merc. is $200+ Good Luck Just a heads up, hope that is not wrong with yours !!

Well if your ECU mapping is for 93, and your running 90. There is a good chance you could be seeing knock. Ecu pulls timing which results in a rich condition.

First think first is to remove the 90 and Put 93 Octane in like your mapped for before you do damage.

With 93 the soot was 2x as much. We do not run it hard at all and seldom in temps over 85-87 here in MI. it has a 120 T-Stat as recommended by whipple, which may be contributing to the last bit of soot i now see. t is run at less than 1/2 throttle... The push rods are interesting. Also I am aware that changing spark plugs won't fix the condition. I had suspected fuel injectors being the problem so I ran FI cleaner through it, then changed plugs to see what I end up with. The soot has gone WAY down. Almost not there, but still present. What is there now may be normal for the 496.... As I haven't really heard of anyone who has zero soot with that motor. I will do a plug check again this week. As far as bad push rods, since the mis has cleared up with the FI cleaner, I have to assume the pushrods are ok, but yes, my motor is an 03.

My 496 MAG was built in Sept. 2003. The only time you will see a really, really faint hint of soot on the transom is if I run in cold temps early or late in the year. There is never a hint of soot anywhere during the normal boating season.

here another thing to think about ,,you had Dustin at Whipple recalibrate your original ecu with a stage2 program ,,that program is meant to run on a 496 mag HO engine 425 hp,,if I am not mistaking you have a 496mag 375 hp engine,,you need to have the ecu reprogramed with the latest cal for a 496 mag with latest anti soot calabrations and start running 87 octane like its programed to do..

I put my ear up to the screen and I could not hear anything your plugs said, fail!

I agree with giving Dustin a call with the serial numbers off your computers to see what set up it was calibrated for. Ask which plugs, thermostat and octane fuel to run.
Also if you are using an oiled style air filter/arrestor make sure you clean it with the cleaning kit once a season.
BTW, I like the NGK plugs better.