2001 RX DI slow after replacing Rectifier, batter

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I had the Maintenance light flashing, the 12v. So I put in a new battery, tested, and it was slower, and maintenance flashing. So I replaced the rectifier. Now the maintenance and beep is gone, but it wont go faster than 35, and seems to be half power.
The max RPM now is 4560, does not have the whole shot, no power at any rpm, or at any time. At first I didnt hear any misses in the firing, but after riding at a very steady speed in calm water I noticed some evry once in a while.

Any ideas? I rode it in limp mode for about 45 minutes, then went home and started the process to troubleshoot.
If the light is not flashing, then you are not in limp mode. What is your compression? Have you changed your plugs?
Riding in Limp mode for any length of time isn't good. (other than getting back to shore)

I would start by checking your compression, and check to see if the RAVE valves are working. (When was the last time they were cleaned?)
It has only 42 hours. It had full power when I put it on the trailer, just went into limp mode at about 3500 rpm, if I let it drop below 2000 rpm, it would have full power again until limp mode kicked in.
I should have replaced the plugs, just in case, but......full power when trailered on tues, replaced the battery and wed it had half power. I doubt its a plug. But they are hard to figure out. Oh, and its a 2002, I posted wrong initially.
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I took it to the dealership, and they said it should be simple, and they would get to it next morning. Well at 5:00 they had not touched it. So I picked it up, with two plugs and we will see tomorrow.
Let me know what you find out Brockin. I'm having the same issue with my 2000. Worked great one day, then the next half power. 28 hours on a top end rebuild, new battery, and spark plugs. But I just bought it and rode 4 hours before this. Very discouraging and I'm worried about getting taken to the cleaners by a dealer without a clue to what might be causing this. :banghead: Thanks!
I'm sort of in the same boat. Have an 01 rx di and had some issues last year. the 12v Low Maintenance light was flashing (extremely low battery voltage). The previous owner said it might need a new battery. Well last year we charged the old battery and the ski ran fine, then again the 12 v low maintenance started to flash, so i would just put around for 10 minutes and then rev it up and the code would stop flashing and ski ran great (i'm assuming the charging system is working?) This year i put in a new battery and trickle charged it the night before riding it. Took the ski out this weekend, started right up, ran mint for the day and then we put it on the lift. The next day we went to take it out, it started and again the 12v low maintenance code came on, along with the 2 sec. beep every 58 seconds. OK, so now i know it wasn't the battery last year, and the cables and battery terminals aren't corroded. Putted around for ten minutes, then started to rev it up and the code went away. Checked the terminal voltage and it read 12.6 while the ski was off. I looked through the service manual and the only two things that could still cause this code could be the rectifier or the magneto, since the battery is good, fuse is good and no connections look like they're in bad shape. My question is, would the code go away if either of these two parts were bad?
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I bought mine with the light flashing thinking I could figure it out. Well, the rectifier actually fixed the problem, but it was sold to me with only the trainer key, and I was none the wiser. This is why it only went 30 mph or so. Reprogrammed the key, and am supposed to pick it up tomorrow. All is supposed to be corrected.? Live and learn,huh.
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