Rider675,
I know bluntcut, bgentry, and Obsessed with Edges are all probably more knowledgeable than I am - I've seen their posts on different threads - but I still wanted to give this problem a shot based on my experience. Their suggestions, in a sense, are to create a type of micro-serrations on your blade. I agree this approach should work; we've all seen so called tomato knives, which are generally cheap and thin serrated blades.
I understand where bgentry's point #1 is coming from, but since your blade is very thin, if it is sharp it should slice the tomato. A razor is very smooth but it will also slice any tomato, even an almost rotten one (they're harder to cut).
You wrote "maybe im not using enough pressure with fine and uf stones." But in my experience, it's always better to use a technique that applies firm strokes with light pressure. In other words, more strokes with less pressure. This makes it easier to apply the pressure evenly throughout the stroke.
You also mentioned spending 1-2 hours reprofiling each time. That's a lot of time, even on a Sharpmaker, which I don't think is intended for that task. I hope you're cleaning the rods to restore the surface.
There are some very good threads on sharpening you can check out. I can also suggest reading the article in the link below, which gives you some theory and practice suggestions, but unfortunately is based on using stones, and you have a Spyderco Sharpmaker. However, most of the practical suggestions can still apply.
http://www.caseyspm.com/Knives.html
The Sharpmaker is great but it's hard to apply firm, but light, even pressure as you work the blade's length down the rods with only one hand holding the knife. Try using one hand on the handle and a guiding hand or finger(s) on the front of the blade, to assure consistent pressure. However, I think this might not be your problem.
I will read on to see what other posts suggest, and the results you get, because I'm intrigued.