I did more searching on the MJLJ route and the DIY kits are NLA. Couldn't find any schematics either. The other issue with the MJLJ on my applications are that both bikes are twin cylinders. One is a 360* parallel twin running a single wasted-spark setup ATM (mechanical advance/trigger) and the other is a 180* motor (a hit-hit-skip-skip motor). Both of these I don't think would work with the MJLJ EDIS setup as EDIS was used for 4, 6 and 8 cylinder applications. Additionally, a regular MS-I is cheaper than the MJLJ available anyways, but the form factor and cost are prohibitive for what I'm looking for.
A cheap voltage converter/regulator can be had for about $9 to clean up and supply sufficient 5v for the Arduino http://www.ebay.com/itm/251155257634?ssPageName=STRK:MEWAX:IT&_trksid=p3984.m1423.l2649 and is also up to exposed element use.
As far as I can figure, I would need a simple input for a TDC indicator (whether points pulled low at TDC, or a trigger wheel input) and a simple logic output to trigger the current transistor controlled HEI module. Add on a MAP sensor and then the table lookup becomes feasible. And all for a lot less than $160 (MS-I/MJLJ) and a heck of a lot smaller/simpler