I'm no expert, but if the problem/characteristic improves (at least temporarily) after a hard stop, I'd lean towards the pads and DakarM's suggestion. Not sure if I've ever driven a car w/ ceramic pads before though so :shrug:

The steps given in the service manual will help at least put you at ease that nothing is wrong if everything checks out.

And I'm pretty sure you're right about the booster and MC being the same for the Si and EX coupe. The EX sedan had a different MC and booster I believe, although the MC being different might have only been b/c it had ABS.