Alrighty, I got the fixed new engine installed over the weekend. So far everything is wonderful. It is like a completely different engine after the repair. MM stood behind me 110% and probably lost their entire profit margin on this engine, and never once asked me to pay for anything. This was all due to a broken valve spring, which isn't even entirely their fault. Despite numerous logistical frustrations with them, it has been a very positive experience working with them, overall. They know their stuff and will gladly talk your ear of about M42 engines.
My suspicion is that the valve spring that broke was partially collapsed from the first start, and that one of the exhaust valves was just never really seating properly, and possibly bouncing. Now, it idles perfectly fine, it runs quieter and it pulls far more smoothly. With the hot cams and pulse chamber intake manifold, it even sounds a lot meaner than the stock one! On top of that, the raspy noises when accelerating are gone, and replaced with a slight whine. I think that all of us have assumed that the raspy noises were from the exhaust, but I am really thinking that they come from the timing chain's idler sprocket. Playing with the one from my old engine, it is entirely conceivable that that sprocket's bearings make all that noise. Now, I just have a neat whine as the chain moves over an M44 rubber guide rail in that place. No more sprocket!
As of now, I have only put maybe 40-50 miles on it. Wedding plans and business travel keep me super busy, and I don't expect to do a lot of driving for the next couple of months. Still, I have given it a few WOT runs up to 5000RPM and it pulls really hard and smoothly. This thing has a lot more mid-range torque than the stock M42, and it just feels great. The 11lb M20 flywheel that is in there also makes it feel really alive. One I get 1000 or so miles on it, I will put in some 15W-50 full synthetic oil and run it up to redline. THAT should be a lot of fun!
I am still hesitant to let my guard down with this car, sadly, but I am fairly optimistic that future problems will be with things other than the engine. Really, my only concern now is surrounding the transmission. At least those are cheap and plentiful, and relatively easy to replace. At idle with the clutch pedal up, I get a lot of mechanical noise from the input shaft. Both of my stock 318iS' were like this, but it is now a lot louder. This might be due to the lighter flywheel, and the fact that the new engine runs so quiet that the input shaft noise appears louder.
I swear that I am also getting some sort of vibration noise on the highway, and it sort of seems RPM related, but it is totally intermittent and I don't seem to get it around town. It may just be the worn out solid rear sway bar links, which ARE noisy, hitting uneven patches in the road. When I was putting the driveshaft back together under the car I was hot, tired and pissed off. As far as I can remember, I got the little white alignment marks aligned properly. I put a driveshaft back together improperly once in 2004 and it was immediately apparent at any speed in excess of 35mph. If it is misaligned now, it is only so by 1 spline, but I would assume that at 75mph it would make for a pronounced vibration. Anyway, I am probably over-thinking things. No more wrenching until 2013!