The low limit stop on the 8050 Di2 is electronic. The upper stop is an adjustment screw.
Put the bike in the small chainring and the largest cog.
To adjust the low limit press and hold the junction box button till you get the red light (half second or so). Then push the left shift lever button until there is a clearance of .5 mm between the inner FD plate and the chain.
Press the button on the junction twice when you're there, and you're done when the lights go off. I just installed mine last week. Adjusting is simple.
http://si.shimano.com/pdfs/dm/DM-R8050-01-ENG.pdf