I currently daily an 89 Civic rt4WD model with an automatic transmission. I hear that the manual swap for the 6 speed with the 4wd is a pain. Would it be easier just to 5 speed swap it and convert it to FWD?, If so then how manual transmissions fit into the D16A6? I don't care too much about losing the 4WD, I just want a manual to have more fun driving the car.

 

I dont know about a pain. There are a number of people who have done this. The real issue is you will need a complete donor car for the parts as there are many different parts needed and, as you probably already know, they are pretty much unobtainium ala carte.