Why you make it so confusing one 

EW timeline is direct sequel from TV series, but just imagine the Gundams they've been using in the tv series to have always been the EW designs (except for 1st wing, Shenlong and Deathcythe; the EW designs replace their second version which were Zero, Altron and D-hell). Basically the EW customs are the suits they've been using for the latter half of the series canon wise.

Take out TV designs, replace with EW designs to sell more kits. No changes in timeline.

Ein will later create a mass destruction machine to destroy tekkadan and anything in his way and all others need to stop him,  perhaps?

could be the spine already damaged the nerve, so if recovered, his limbs might useless because cannot move and control MS.

so my best guess is they use Hallelujah (i forget the name) system to make brain direct input command to MS.

Looking back.. IBO seems to be the only Gundam series that did not have any beam weaponry

this episode the last part definitely is a doujin material.