I thought I knew exactly what I needed, but I was slightly off. The bolts were just a hair too long, so I had to quickly find a hardened washer to throw under the bolts. In too much of a hurry to go back to ARP, I hit McFadden Dale industrial hardware (if you're in Southern California, this place has an incredible bolt selection) and grabbed some 7/16 Grade 8 washers.
The problem with mixing metric and standard hardware, is nothing ever fits quite right. The washer is almost 12mm, but not quite. Look closely, and the washer never sits flush against the head of the bolt.
The problem is this fillet at the base of the bolt head. A fillet that's critical for maximum bolt strength, of course.
So, what started out as a simple, super-paranoid bolt swap ended up as a long night of meticulously filing a chamfer into each of the hardened washers with a Harbor Freight file. Good times!
That problem we had with the clutch not disengaging? This was it.
The shaft that holds the flywheel adaptor was a few thousandths too long. The flywheel itself is in the right place, and the clutch itself actually works perfectly, but the end of this shaft takes up the same real estate that's normally a big recess in the back of the Miata crank. The transmission input shaft pokes through the flywheel (where it's supported by the pilot bearing) and then just passes through into a hole in the back of the crank. This is a very loose-tolerance hole just intended to leave room. Precise location is done by the pilot bearing itself. Apparently we had underestimated the clearance needed here by just a few thousandths and the input shaft was pressing hard against the back of the shaft.
The contract pressure between the nose of the input shaft and the back of the Miatabusa shaft was hard enough to lock the two together against our attempts to push start, but once the engine was actually running, the shafts quickly machined each other until there was enough clearance for the clutch to work.
We should have noticed this during assembly. In fact, we had to use the bellhousing bolts to pull the engine and transmission together the last fraction of an inch. This happens a lot, though, when engine and trans are slightly misaligned and the alignment dowels are hanging up. We assumed this was what we were dealing with at the time.
We assumed wrong.
The quick fix this time was to just hit the nose of the input shaft with a grinder to make a little room. The next shaft will have a bit more clearance built in.