@jzelt -
I'm really sorry I didn't see your post earlier. I'm going to reply on the assumption that this information might help someone else, even if it's too late to help you.
I had problems almost identical to yours. After replacing everything in the obvious chain of related parts (fuel pump, fuel/water separator, injectors which are ungodly expensive for all eight, other things I cannot remember -- over $3,000 by the time I was done). After all of this work and over a month of re-testing with full-blown "water tests", I finally learned it was a < $50 part.
As it turns out, there is a "fuel pickup tube" in the fuel tank that can come apart, or spring a *very small* leak over the years.
Here's the really interesting part: When you run the boat on land or to show your mechanic, it might run fine depending on how minor the problem. It won't be until your boat is *under load* (for example, a water test) that you'll see the issue, because it needs more gas, and a minor leak at this fuel-pickup becomes an issue.
We don't have a SkiersChoice mechanic locally here in West Palm Beach, FL. Technically we do have one (according to the part-time dealer here), but this mechanic doesn't return calls and he wants nothing to do with SkiersChoice boats as he's primarily doing much larger Ocean Yatchs now days. Therefore, I get my boat serviced by the local Mastercraft dealer, which I'm very happy with -- they really do great work. Sidenote: They've never given me the "Mastercarft is better than Supra" story or condescending attitude, not once in all of my visits.
My dealer called SC to order this part, and from what I understand SC does not stock it, but it's a standard part from the big wholesale marine supply place most of these guys use (I forget the name off the top of my head). My dealer told me that this part could theoretically be repaired, but in their experience, because it's in the tank, it just comes undone, no matter how much they do to re-affix it, and no matter what special equipment they use.
I'll send you a link to a similar part here (although I don't believe it's the same). The reason SC's part is unique on my Supra Launch 21V, is that it's larger than the conventional part on most other boats. For example, the link I'm attaching here is a photo of a tube with a 7/16" threaded fitting to attach the fuel-line. If I remember right, the line in my 21V was larger, something like 3/4". Whatever the size was, it was larger and less conventional.
Here's a link to the similar part, so that you can get an idea of the appearance:
http://greatlakesskipper.com/en_us/s...nk-pickup-tube
I hope this post can save someone else thousands of dollars, like it would have done for me, had I found it before replacing more expensive items!
Also, write back, and let me know if you ever fixed your issue without this. I'm curious, if this problem was not related, what else it could have been.