I've had to deal with this problem myself, I opted to rebuild my own engine and I'm glad I did.
Here's the real story, and BTW I posted a huge write up on this on HCS with all the technical details. So I will attempt to summarize this a bit.
In the 2004 model year Polaris was trying to squeeze as much power as they could out of the 550 fan cooled power plant. They did a number of things wrong that lead to a SLEW of people experiencing a catastrophic engine failure, either a seized engine or a melted down piston. Reasons why, the tolerance from the factory of piston to cylinder wall clearance was to tight. The throttle band had a lean spot between 1/4 and 1/2 throttle. The exhaust system muffler located right next to the air intake for the cooling fan was not insulated, the edge chassis design did not allow for enough air flow to keep the engine compartment cool enough.
So what did Polaris do to address this? Well first of all unless the sled blew it's engine within the first year of ownership (some did, others did not) they would not do anything to fix them. They changed the following items which includes all the way up to this year's model. I'll start from the oldest update though the latest.
-Changed the piston to wall clearance IF you use OEM pistons (I'll get to that later)
-Put out new specs for changing the main jets in both carbs, they spec differently between the two essentially creating an over richer mixture
-Put out a new spec for the jet needles, again jumping the size
-Put out a new spec for the needles and adjustment for the retention clips
-Put out a new spec for the air/fuel ratio adjustment on each carb
-Started to put insulation on the exhaust pipe with stainless steel covering
-recommended cutting a vent port in the front of the belly pan for better air circulation
-put on a new oil pump relocation kit which they claim fixes another problem of air pockets being created in the oil injection system at low RPM operation
-for rental fleet put out a new air intake system that has a dust that covers the air intake on the side of the engine and has a duct which must be installed in the hood of the sled. Got to cut a hole in the middle of the hood to install it, the idea I guess is to pull raw air from outside the engine compartment no doubt do to the lack of air flow through the belly pan during operation
-Came out either last year or this year with a new teflon coating that is supposed to help dissipate heat.
-This year they also added some new heat sheilds on the exhaust system and the air vent in the front of the belly pan is now standard.
OK so what does this all mean, well bottom line the engine has problems keeping cool and the lean jetting just makes it that much worse.
My engine melted down, I blew a hole through one of my pistons. Reason why I did the work my self, a big Polaris dealer (WILL NOT NAME NAMES) diagnosed the problem which is fine, but was only going to fix the bad piston and only bore that side if needed. I cannot believe a dealer of their stature would EVER consider doing something so irresponsible. OK I digress, I'm an ex mechanic and figured I'd tackle the job myself and that way I know it's done right.
First off the ENTIRE engine must be disassembled, anyone who suggests otherwise I would be hesitant to have them do the work. Secondly and I'm glad I had this conversation, the guy who did the machine work for me insisted that I consider using Weisco pistons versus OEMs, reason OEM Polaris pistions are cast which makes them inherently weaker and not necessarily uniform in regards to integrity. Weisco pistons are forged and milled so they are much stronger and of far better quality. The piston to wall clearance of the Weisco pistons are also greater than that of Polaris so it assists in keeping the potential of heat build up and seizure at a minimum. Along with the rejetting that cured my problems. I did cut a vent in the front of my belly pan. I only use synthetic 2 cycle oil and did slightly increase the oil flow to the engine.
My general observations are from 2000 when the 550 was introduced it was bullet proof. In 2004 to now the combination of engine tweaks from the factory and the fact the edge does not have as good air flow has been a huge problem. IF the engine is fixed correctly and enough air gets into the belly pan they are fine, IE put a vent in the front of the belly pan. If none of this has been done I would highly suggest you do or face blowing the engine. If you are looking at a used one be sure it's been modified per spec or you are buying a potential problem sled. I've seen enough of these go bad and talked to a TON of people due to my posting on HCS (hardcore sledder) who have asked me about the proper way to fix them. There is no reason to be scared of this engine but you've got to be 100% sure it's been fixed properly.
BTW if anyone is interested I do have my 04 2up 550 touring for sale. It's MINT and it's been fixed right. Not dumping it due to the engine, rather I'm about to buy another 1 up sled, don't need the 2up anymore.
Finally if anyone has any questions or wants more details feel free to contact me as I have a boat load of information to share. I've also been approached several times to rebuild these engines. The only problem with that is to do it right costs a lot of money, it set me back 1K between the machine shop and parts, and my labor of course was free. If I ever were to consider doing it I don't think I could do it at a competitive price, however I will say that it's not a complicated job and can be done by anyone with basic mechanical skills.
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