Two missing teeth are not uncommon on high compression engines, but IIRC the teeth are missing 180deg from each other? This is similar to what Renault were doing at the time, it lets the ECU know that theres a cylinder at TDC, but it doesnt know which one - the distributor sorts that out.
Trigger wheels are often a 'black art' and welding one on may cause problems that we can't even guess at.
The position of the missing tooth is not so important as we can set a trigger_tooth in the configuration, then define its position BTDC.
After talking to the guys who've done a number of installs with custom triggers I personally would do one of two things:
a) Cut off all the teeth except for one either side that will pass the sensor 90deg BTDC, and sort a cam sensor. I'd use the Honeywell 1GT1
http://www.pe-ltd.com/Downloads/hall_effect_GT1.pdf sensors for this.
b) Use a known good trigger pulley setup, I know that Chris Good is running a 36-1 on his MS'ed Mini