yea, you can keep the cruise and ac, i dont know why'd you loose AC. The C-spec (<---hahhahhahhaa) SiR (US Si) has AC, that car has a B16 as well. So did the del Sol VTEC, b16 w/AC and cruise.
Anywho, with the auto-manual you loose 2 things. cruise and reverse lights. but, they can be "hard" wired into the existing system to work again.
also, when you go to swap, make sure you got a spare car, it may be down for a few weeks. and DON NOT CUT THE WIRING INSIDE THE CAR, UNPLUG THEN REMOVE IT. A lot of the facotry wiring has to stay so you can splice some wires, wire some together.. etc...
I would go take some pictures, but well the fucking cam. phone is gone. ahhhh, stupid girlfriend.
Ill get some pic's, it may or may not be the same.
I hate to say it, but there's a link on Honda-Tech, for auto-manual in an EK (96-00) Civic.
You may find this valuable.