I had one of the $20 Accell Super Coils on mine for a while, and it definitely wouldn't fit in the stock location. Too big. I mounted it on the back wall of the engine compartment. I took it out, because I felt that any possible gain (I couldn't tell) wasn't worth the hassles of working around it. I think putting it in the trunk would fix that problem, but would then cause you to have issues with the main coil-to-distributor cap wire being so long (maybe not a problem, but...), and potentially getting damaged, depending on how you got it to through the trunk wall.
I think MSD makes one that fits in the stock location, but I'm really not sure.