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As long as everything was measured and checked your piston assembly should drop down the cylinder with little to no trouble. 
Here’s what the underside of your engine should look like. See why you want to make sure your crank journal is at the bottom of the stroke? Imagine if that rod end scratched the journal… back to the machine shop! 
Cap her off, torque her down and repeat 5 more times…
…congratulations! You now have 3.2 liters of fun. 
But we’re not done yet! Since we elected to go with ARP main studs which happen to be a bit longer, notching of the oil scraper was a necessity. 
With the whole “while we’re in there” mentality we got some new OE timing chains from Pelican Parts. Pelican Parts has been a great asset as their office is literally 10 minutes from the palatial MotoIQ Headquarters, and they've usually had everything we needed in stock. 
2 comments
Not sure when this was posted but thanks! I’ve had a lot of BMWs in the past but nothing later than an e30 and am now looking into a ’96 e36 328is. I’ve been searching for REAL information about a sensible but effective build to reach the M series performance levels and this is the first REAL build I’ve found that speaks my language (brought up on hot rods and muscle cars) My main question is how can you increase the stroke without shortening either the rods or piston pin height?? Or do the M3 pistons have a different pin placement than the m50/52? (I was trying to avoid using all the m50 etc, frankly you need a damn score card to keep track of it all.
One of the first questions I had after reviewing engine specs was if the M car crank will fit the IS block and cool – yes it will! Another was how much the cast iron blocks can be overbored another point! So now I can toss out all that fan boy (never actually built a motor but know it all) “info” and get back to a proper build, bore, stroke, pistons, cams and go. One question if you are still reading… actually I am going to add this up top. RE pistons 323 328 vs M3 seems to me you can’t increase the stroke without shortening something either the rod length or piston pin height.?
Thank y’all for this write up. Restoring my M3 (minus stuff that weighs too much) and my dad rebuilt my motor for Christmas from this post. Big time.