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Figured I'd re-introduce myself after posting that I was thinking of getting back in an R53 about a month or so ago. I ended up buying a 2005 with 183k miles on it, but a 105k motor was swapped in about 20k miles ago (along with new clutch, SC service, timing chain). Even has JCW exhaust, Alta 15% pulley, and Alta intake. Seemed to be a pretty solid car, with very little rust issues, in spite of the mileage. But oh man, has this thing been fighting me, lol.
First major issue was even before I got it on the road. I started it one day and it made a racket, like a death rattle x10. shut it off, and started it again, still made the racket but as I was pulling into the shop, the noise completely stopped and it sounded perfect. Hmmm... Started it again and it sounded fine. Thought maybe it was the timing chain tensioner. I pulled it and it did seem a little sticky, so ordered a new one. I continued doing what I originally intended to do (front lower control arm bushings, and power steering reservoir hoses). Got that done, fired it up again, this time it made that racket again. Shut it off and it tried again and it made some crazy sound, and the starter freewheeled. Now I'm thinking catastrophic failure of the timing chain, guides, crankshaft, the worst. Pulled the valve cover, everything looked fine. Dropped the oil pan, expecting to find broken chain guides, and again nothing. No sludge, no plastic, no metal, no nothing, just clean oil. Started turning the crank by hand with a ratchet and could hear some rattling over on the driver side. Then the lightbulb went off in my head. The starter had gotten stuck and wouldn't disengage. Which would explain the electrical burning smell I noticed when the engine first made the racket. Ordered a starter, and sure enough, the old one came out in two pieces. Thankfully it was a clean break and nothing fell into the bellhousing. Also did new valve cover hardware and gasket and oil pan gasket since I had that all apart.
Was running and driving great for a week or two, got my sound system in, even retrofitted oem steering controls and got them to work with my aftermarket radio. Then a new noise appeared. sort of a rattling/bearing kind of sound. Figured it wasn't the chain since i had a brand new tensioner and the chain and guides all looked good. I thought it had to be the supercharger. With the belt removed, all the pulleys spun fine, but I could feel a little bit of slop in the SC. Ordered a new SC, and water pump, got that all in and the noise was still there! Damn. Turns out it was the alternator all along. I noticed a crack in the housing when I took it out to do the SC so was planning on a new one anyway. It was deceiving because when i spun it on a drill, it sounded fine, until i put some sideways pressure on it (simulating belt tension), then it started making noises.
I still need to change the O rings on the oil cooler which I think is my last leak. Oddly enough, where the oil filter housing meets the block seems dry. Also still needs a windshield, and has a dent on the bonnet that needs fixing, but for now all is well. I had new 2003 and 2005 R53s back in the day and forgot how much fun they are. In spite all the hiccups, I don't regret getting a 20 year old Mini!