When asking for technical help at the very least let us know the version of firmware you are running.Cliff's Calibration (Mapping) Guide is a MUST READ: http://www.vemssupport.com/forum/index.php/topic,97.0.html
set ignition outputs to 05..00, set output channels all to 0(35), set reftooth h1 table from top to bottom: 0 40 20 0 40 20, check h2 that there is ign on top 8 and 0 on bottom 8 selection.
Yes just unhook both wires from your coil and use a beep test on the signal wire to groundthen when the ecu grounds to create a signal you´ll hear the beeping.
You have a few choices:If you have a channel on the VEMS that is populated with an IGBT you could connect directly to pin B on the coil.If you have "logic" (gate wired to source on the board) then you can use that to drive pin4 of the Electronic Ignition Module (N1).Or you might be able to use the stepper output to drive pin4.