tryin to break in new engine, ruff idle

Try finish breaking that cam in,since you have a timing light set it so it is under your wiper blade with a zip tie holding the trigger and all cables out of the way of header,fan,etc...and pointed to you in the driver seat.
You should be see steady blinking light,if when it start to act up and it is still blink steady,then may not be ignition problem but if it start being erratic you found your problem.
Keep us posted,
TXDart
P.S. Is your orange box attach to the firewall real good, it is grounded to the body thru the bolts that attach it.