Engine Rebuild
Why build an engine? It can be argued that a miata engine is so cheap, that it's not cost effective. Just keep running boost until it blows! For the most part, that is true. However, the labor and time it takes to find and swap an engine can be intensive. My philosophy is do it once, and do it right.
I ran a stock engine with a FMIII at 14 psi. The little motor put out 270 rwhp @ 14 psi. Not too shabby! However, I decided to build the motor and turn up the boost.
The block was hot tanked to clean the sludge from the oil and water passages. The cylinders were bored ~0.040" over. After honing, the cylinder to wall clearance was 0.0035". The block was decked 0.020". Installed in the block were JE pistons, Pauter rods, MBSP, and ARP head/main studs.
The head received a three angle valve job, port and polish, and 99 cams/solid lifters. The combustion chamber was also reworked slightly.
Running the "little" BBB T28 at 18 psi did not make much more top end power, but made LOTS more mid-range torque. Hmmm... time for a bigger turbo!
Tranny Rebuild
I decided to cryo treat the transmission. Miata trannies are notoriously weak when pushing over 250 rwhp (well, it's more torque related than hp..)
For the cryo treatment, the tranny has to come apart. I decided to go ahead and get new synchros, and put in the RX7 taller 5th gear.
The tranny ran great for a few thousand miles, but finally gave up after a hard 2-3 upshift. 303 ft-lbs of torque can do that.
Next, I'm going to try a 6 speed miata tranny. The 6 speed has a much stronger case compared to the 5 speed. The stronger case will flex less and therefore keep the gears orientated properly.
If the 6 speed does not work, I will try a RX7 TII tranny. I do not wish to give up the PPF, but I may not have a choice.
UPDATE (11/24/2003)
6 speed transmission and 3.636 rear end gear are installed along with a Toda chromolly flywheel and Bully 6 puck sprung sintered iron clutch. So far, the setup is reliable, keep your fingers crossed.
Toda flywheel:

UPDATE (5/27/2004)
6 speed transmission and 3.636 rear end still holding up to the power. Got two BFG drag radials recently but haven't been to the drag strip.
One problem with the 3.636 rear end is the speedometer is off ~11%. Miatas with a 4.1 rear end came with a 22T speedo gear. The only Miatas with a 3.636 are from Australia, and they had an electronic speedo drive (no speedo cable, same as all 99+ miatas), so there was no easy bolt in solution for us M1 Miata owners. Just recently, with a lot of help from some folks on miata.net, we found a suitable speedo gear:
M502-17-441 19T gear from a AT 929
Mated with a 2nd gen RX7 speedo drive "sleeve", this gives me a fairly accurate speedometer.
Another option is:
M503-17-441 20T gear from a AT 929