You can take the car to the dealer to have them reprogram your car which will cost about 2 or 3hrs labor and it will cost you about $80 for a key give or take. I did not want to take my car to the dealer so I went and got a new ecu.
P13-A12 ECU which is only used for the 1996 prelude SI. Pic below is a picture of the P13-A12 ecu vs the stock H22A4 ecu out of a 97-01 prelude which has the pain in the *** immobilizer. This is the reason why I did not want to use this ecu and my car would not see a dealer to get my keys programmed to work with it so that's where the P13-A12 came in. It's rare and highly sought after, 96 was the only year the obd2 p13 ecu was made and it didnt have an immobilizer in it out if 1996 OBD2 USDM 2.2L preludes most junk yards know it's rare and will charge you out the *** but I might be able to find one but it took me a few months of looking to get one at a good price.
You'll also need to buy a conversion harness if you plan to use the P13-A12 ECU which converts your car from a OBD2b to a OBD2A, this harness costs about $100-$150 at most it depends where you buy yours but Rywire sells it just for example.
thanks for the reply, i've been doing some research and a couple of people said to convert to a obd1 ecu, the harness is 75 on rywire and i've seen quite a few ecu's on ebay rangeing from 65-200 depending on mods to the ecu. it just sucks i have to give up the added security of the immoblizer, but it'll be expensive converting the obd2 ecu.
It won't be that much more really, if your not wanting to stay OBD2 I can understand as OBD1 is more better for tunning and making power so you have options good luck with everything.