ooookay, if you plan on going the hard route and putting an obd0 B16A in an ek (96-98) civic, theres a lot of crap you're gonna need to make it work.
first, you're gonna need the motor (duh). go ahead and get a bare longblock, you're gonna replace everything else anyways. you're gonna need to buy an obd2 intake manifold, throttle body, injectors, distributor, alternator, header from a 99-00 si (unless you've got an aftermarket one)and you should go ahead and get an obd2 transmission (i used an LS, but they suck so try not to get one). you CAN use your stock wiring harness, but you'll have to add vtec, knock sensor, and vtec oil psi switch wires, as well as re-wire your IACV. your best bet here is to get a 96-98 EX vtec harness. also, you're gonna need to get either an obd1 vtec ecu (p28, p30) or an obd2b Si ecu (p2t). a p30 would probably be best, since obd2 sucks. depending on what ecu you're gonna use, you'll have to get a jumper that converts from your car (obd2a) to the ecu (obd1 or obd2b). you'll also want to get a new clutch (Exedy rules), and I went ahead and got an ITR flywheel from ebay.
mount-wise, you'll use your stock driver's side and passenger side mounts, and you're gonna have to get a B-series rear tranny mount. I just got the wishbone mount (that bolts onto the tranny) with my transmission. I used a grinder to make my stock urethane mount narrower (the LS mount is narrower than the stock d-series mount), but you can just get the urethane mount from an integra or an si and it should work. I had to flip the rear urethane mount around, too, for the motor to fit right, and was only able to bolt 2 bolts in, and youll probably have to do the same. for your axles/IM shaft just get them from a 99-00 Si. shift linkage wise you'll need to pull it from whatever car you got the tranny from.
now, as far as putting everything together it shold be pretty easy. put everything on the motor BEFORE you put it in the car. it's a bitch getting to everything to plug up the harness. everything should plug in, you MIGHT have to extend some wires. make sure to use new gaskets, a Hondata IM gasket is an awesome thing to use here.
MAKE SURE NOT TO PUT YOUR CLUTCH IN BACKWARDS
now that you've got your IM, dizzy, alternator, tranny and what all else on the motor, drop it in. it should fit right in. always bolt the back mount first. then, get under there and connect the shift linkage and put on the axles. then, put the wheels back on, go pump the hell outta the brakes and the clutch to get pressure back, and check your fluids (trans., engine oil, coolant). then run your harness back through the firewall, plug the green plug to the dash harness, plug in your jumper, and plug in the ecu (you DID get obd1, didn't you???). now connect the battery cable, and you SHOULD have a working swap.
if for some unknown reason youre using an obd2 si ecu, youre gonna throw a code for the crank angle sensor. obd0/1 motors didnt have these. disregard it.
let me know if you have any questions.