I dont know if this will help you any, but I can tell you my plans for my EX.
First, Im just going to concentrate on handling aspects. (lowering, strut ties, sway bars, wheels, maybe brakes, etc.)
Then Ill decide which way to go as far as power is concerned. Im leaning toward supercharging the SOHC, but having an automatic complicates things, and I may decide to swap as well. Which is why I have vowed not to get any more go-fast goodies, until the rest of the package is up to speed first. I did break down and buy an AEM cold air, but thats the last thing, I swear! Since it sounds like you are leaning more toward swapping, perhaps you should save the money you spend on headers and exhaust (since they wouldnt be compatible with the new engine anyway), that way you can swap that much sooner. I would definitely stay away from any internal stuff and other generally expensive mods, if you really dont know where you plan to go with the engine yet. I wont tell you not to get an intake, since I got one myself and it is nice.
Well, dont know if my rant means jack to you, but just thought I might be able to give you some things to think about.