I have done that swap myself and I know that it's very difficult to do the wiring... If I draw or show some kind of picture I could show you how it done.. since I can't do that I guess I can't help you much...
Remember, when you do the wiring... you'll be running only one O2 sensor so make sure that you're using the right o2 sensor... I recommend you to get an OBD 1 integra GSR 94-95 (USA) complete wireharness... Don't forget that you need a OBD1 ecu then if you're using obd1 wireharness.... If you wish to use your wireharness in your car then it'll be more complicated, but it's not impossible.. Just make sure that you know which wire is which.... by the way, just make sure that you get the wiring on the distributor right because they're the most important ones... One more thing, if you're using your wire harness in your civic then you'll have to run a obd2 ecu such as one from 96-98 integra gsr... sorry you can't run the 99-00 honda civic si ecu because they're obd2b so it won't fit the harness...
and hey, you can use the honda civic 99-00 si back bracket mount... if your motor comes with tranny mount then you don't have to worry about getting another tranny mount... if not.. you can just use your old ones for your car, they will fit... however, you'll require to get two new mounts... and they are: the driver side bottom/front block mount, and the passenger bottom/front tranny mount... you don't have to have them right away, but they're necessary if you want to race or anything because if you don't have them then your main driver side mount will break and your motor will jump... a possible block crack where the bolts from the driverside mounts goes to the block could occur... It happened to me so i know...
one more thing, you can use any B-series shift linkage such as Ls, gsr, si, delsol vtec, etc...
however, your stock power steering core will not fit the b-series powersteering pump so don't bother to try... what you could do is get a b-series powersteering core if you want to have powersteering...
sorry can't help you much... and people, if I make a mistake please forgive me because I write this base on my personal experience only....
holy_racer