Congratz on finishing up and being on the road! Has to feel good.
You mentioned turning the wheel to 1/2 lock you get a tire rub. Half lock is mid-travel. Are you turning Left or Right? and once past 1/2 lock all is good?
100mm (3.9") is pretty low and how low is your Bellhousing (that usually gets the abuse)?
Was the car set at 2 finger gap (what most folks run their BDRs at) above the tire when you rec'd w/out the motor and trans? Raising the front does increase the toe in. Have you adjusted the front coilovers to the normal 2 finger gap at the top of the tire with the engine installed? Raising the front of the car does give you more tire /inner fender well clearance. (Rack is in front of the Lower control arms) Marking the tire circumference tread with childrens sidewalk chalk will give you the rub area on the tire and body.
What the LCAs should look like
http://cobracountry.com/cobra4salefo...1a-540x431.jpg
Alignment specs courtesy of Secret Squirrel on this forum.
http://www.clubcobra.com/photopost/d..._Alignment.jpg