couple things - first, PLEASE tell me you are going to run some kind of filters, which means the lid won't fit anyway. Otherwise, kiss those nice engine bearings goodbye. You will be amazed how much dust is in the air even though you don't see it. Also, not that the HP is probably an issue, but changing the height of stacks and filters can make a big diff in HP. On the dyno, had an engine lose 15HP (course, that was on a sprint car motor, so big HP to begin with) just shortening the filters 1". Stack heights also have an effect. Had to shorten because wouldn't fit under the sprint car hood. Course the shorter you go, the worse the losses get.
Secondly, do you have the Electromotive already? I was going to use an Electomotive tho' didn't in the end as was unnecessary cost for what I am doing (anything under 7500rpm or 8000rpm just needs a good ignition box and distributor). Saw an HEI hold up to 7500 on the dyno without any power loss v. a different distributor, tho' coil and box can make a big difference. Latest Crane 6 and LX coil was good for 5HP on one motor over similar MSD setup on the dyno when we checked (about 1yr ago now). Might be worth it to you to save the $$ and put it elsewhere in the car
Anyway, if you already have it, then my plan was to do as implied by others, mount one coil pack where the relay board went and the other where the battery went, then relocate the battery. IMO it is best to remove the relay board altogether, splice or rewire the rear section into the loom and use a one-wire Chevy alternator. Clean setup.