just remember to get rid of the ingnition lock from the auto so you can get the key out

 

auto to manual, not that hard, i have done it twice with no problems. and the second the guy ran the auto ecu, just had to make sure that the computer thought it wasnt in park while driving. keep in mind, you will have to drill two holes to hold the shift linkage up, and to connect the two black wires within the auto shifter assembly, otherwise the car wont start.
one the engine swap part, i just put a b16a2 into a 95 coupe this last weekend. we had problems with the rear engine mount, it was too short and the stock will NOT work, alse the front left engine mount will not work. the other three are fine they swap over. to resovle the engine mount problem, you can either buy the engine mounts for that swap or modify it, the front left one you will have to buy, unless you had a really large drill bit, but anyway on the rear one i cut out the rubber in side the engine mount and moved the center hole, the part that the bolt goes through, all the way forward and filled it in with rubber window sealant, defidently not the best way to do it but it works and the engine it centered as well as steardy. so my idea works but its unprofessional. the other problem that you will run into is the speed sensors are different, you will have to go to a jusk yard and cut the plug from a obd2 civic or integra that has the same plug. and the last modification would be to cut the plasting tubing that covers all the wires around the upper 02 sensor to get the length of the o2 sensor plug longer so that it will connect to the moved o2 sensor location on the b16a2 downpipe behind the oil pan. things you will need for the swap include 99 00 civic si axles, or 94 to 00 integra axles. the same years, shiftlinkage. i think thats it. if im leaving something out im sorry because im summarizing in 5 minutes what i did in 11 hours. hope this hepls