I may be wrong but I've never heard of an EB disconnecting when pushing the clutch. Mine is controlled by the trucks ECM and does not disengage with clutch pedal action - and I'm not sure why it would. There's no reason to have it disengage while your shifting either up or down.
Normally for models earlier than the Common Rails, a switch is attached to the throttle pedal so anytime you have your foot on it, it disengages or engages anytime you take your foot off.
Engine mods have no relation to the EB so your safe there. You do need to have the appropriate valve springs and I don't know if your truck came with them or not. (I think so). The switch under the shift lever works great and is where I put mine. It's very convenient and causes a lot of questions!
I think you'll find you wish you would have put one on sooner and
I can't imagine being without it!
(BTW, it's a "Cummins")
