Doug,
Download this data sheet and take a look.
This is an upgrade to the current 68HC908 chip used in the MegaSquirt.
The current MegaSquirt would benefit from a more powerful chip
as you could then add a MAF and other things without kludging up
the basic MegaSquirt.

It does not make sense to stick with a limited single chipper.
This one looks like the best bet. MC9S08AW60 is 64 pins instead of 42.
You want a single chipper with the most amount of I/O you can find.
That actually makes software easier to write. You can then add the
8 hardware interrupt circuit and make things real easy to program.

http://www.alldatasheet.com/datasheet-pdf/pdf/167748/FREESCALE/MC9S08AW32.html
It has more pins and there are I/O more ports. It is code compatible.
I assume you are getting into 68xxx assemble language programming.

You will have to do a new circuit board but a lot of current MegaSquirt
I/O schematics and ideas can be used.

Paul Lamar