I'll try and make it simple. Starting to get into this MS thing and checking out the output section (fan control). Get confused on where the outputs ARE exactally...

...so I come across this...

...take a look at it, and it's obvious these are some of the differences in the V1.01 and V2.2 boards. What I'm curious of are if the outputs exhist on the 1.01, spacifically X2. Also, a random ground on the board near it would be nice.

 

Those solder pads don't exist on the older boards, but the pads are connected to the adjacent processor pins (X2 -> Pin 38) as shown in the schematics here:
http://www.bgsoflex.com/v22/megasquirt_ShemV2.2.pdf

Although not ideal, you can connect direct to the cpu socket pin from the underside of the board.

 

I'd plan to run on the underside anyway; but you are right about the CPU socket. Shouldn't be a problem w/ the chip removed though right?

So, I think I'm finally getting this figured out.

V1.01 w/ the MSnS-E code in fuel-only. Only things I believe are left are...

2N2222A for fan control [X2 - Pin 38, Ground - Pin 32, Output to DB connector] (it's alright to pull a ground from there yea)
LED's still need to get soldered in
Replace R4 w/ a 47k resistor
flip my MAP to the underside of the board to make it fit my endcaps
and add an external boot-switch so I don't have to have the case apart to put in new code.

I hope I continue to learn from this; this board is full of good resources. Here's a pic of my board btw; I'm pretty proud and can't wait to get it in the car.

 

Looks like you've got it covered. I'd suggest skipping the external boot switch step, though. Most recent code versions include auto bootloader entry via sending a "!!" to MS via serial link. EasyTherm attempts this automatically each time you download, so you should only need to short the boot jumper once, when you switch from the base code to MSnSExtra.

Your board looks good. Component spacing is really generous on those early boards, which makes the soldering job much easier.