I'll point out that an advantage of ordering options with the car is that when the car arrives they will have already been pre-fit and installed by ERA with some exceptions (fabric top, outside mirror, seat belts, etc). But to answer your question:
At the time you order you need to have the engine and transmission pinned down so they can determine the correct mounts, headers, speedometer cable, & driveshaft to send. If you think you may need it, order the upgraded cooling fan initially to save the expense of the standard one. Five or six pin wheels needs to be settled up front as well as any brake upgrades from the standard package. If you are seeking any seat modifications such as trimming the thickness of the bottom cushion to sit lower, that needs to be addressed when ordering. If you want the Smith gages I would order them initially as you will otherwise have the S&W gages as excess. If you want a trunk mounted battery I would order that up front.
The heater and defroster and
oil cooler should not be a problem to add later but I would ask ERA to pre-drill the holes for the heater pipes. The wiring harness is pretty much set up to handle all the electrical options but if you plan to add a remotely mounted MSD box in the glove box or something, I would discuss that with them.
I'm sure to be missing a couple items that others will pick up on.