If you have an original running car the EWS shouldn't present a massive issue as long as electrically it's all hooked back up again. I've done an engine swap on an E36 with my brother from 4 -> 6 cylinders and that needed the EWS box / ignition sensor etc swapping over. It did cause a problem initially but worked after making sure everything was in it's correct place.
I think everyone else has covered all the important bits. Unless things have changed the 'manual' is not overly useful as it's for the ford version and what's presented on the CD is about 30 images.
Several builder have extensive build logs that will help a lot. We here can answer most questions between us.
It will take time, a lot of consideration and planning the best way to do things. It's not one you can build in a year unless you have a lot of time. Mine was on the road in 3 years and painted with an engine rebuild / stroke in 5 ish.
I will say from a driving perspective it was well worth the swearing
And my site is here:
http://www.msportster.co.uk - I've also assembled a list of useful links:
http://www.msportster.co.uk/links/