Stealer Ships?......
I'll try not to get on my soap box but as Ryan said, your problem is the stealership you bought it from. They probably were kissing your boots the entire time you were shopping for it, then as soon as you put your John Hancock on that contract, you were yesterdays news. They get their money off the top.
You could continue to take it back ,time after time but you'd probably have a lot less hair or have used a lot of choice words, you wouldn't normally use by the time it was fixed. If they fixed it at all. Why continue to waste your time. Lets fix it then you can go back and tell them what was wrong (that info you got from a "real seadoo mechanic!".....
First, I'd check to make sure your bailer siphon tubes are in place. There have been a few posts where the ski had lost them. They are removable but once in place, should not come out. They are listed as part #28
http://partsfinder.onlinemicrofiche.com/seadooforums/Seadoo_oem/Seadoo_PWC.asp?Type=13&A=161&B=14 and work on the "eductor" principle for creating a vacuum on two lines to draw water from your hull.
These lines come in from the back of the hull, where the pumps two venturi lines come in and go to your drain plugs. One on each side.
What you'll be looking for is that the lines come in and up, making a "U" and back down to the plugs. The reason you need to make sure they come in and up is because if they've fallen into the hull, after you come off plane, they will bring water in the reverse direction, back through the bailers. You'll also see a 90* nipple where they come to the top of the hull, tied in place usually with tie wraps.
There are other things of more concern. The O.P.A.S (off power assited steering) system has thru hull fittings and has water connections. If a bushing or something is amiss, you'l get water in the hull. This, you will need to bring into the stealership and point it out. Grab them by the back of the head and shove their nose down to the part you found leaking.
Like sporsterjoel said, a good way to test is to tie up to dock somewhere and power up with the seat off. You don't need WOT, but some power up to search and look. Have a flashlight and mirror handy. I would be lost without my mirror. Being able to cock it sideways in the bottom of the hull, using my flashlight to light it up and look under the engine and toward the O.P.A.S. system.
There are many areas outside these two that I've discussed. So, take your time and look over all. If you have problems, check the few that we've listed here, come back and we'll go over a few more things.
I see you posted while I was making this post. A bilge pump should not be needed if it's working correctly. I would have never paid them guys a penny!....it's their job to satisfy a customer. I could see it if this was a 2000 model.
If your having probs only on the chop, then is it possible your busting waves into the vents and not staying on plane long enough to drain the hull? You do have to be on plane for the bailer system to work.