just had a b16a(2) with lsd installed and when I'm really getting on it the passenger side vibrates. I'm going to jack it up in the morning to make sure everything is tight it isnt even a real bad vibration just annoying and goes away once i'm up to speed or i get off the gas. i have a cx ek , rims and tires are only a few months old and in great shape, new brakes in the front too aboout a month ago. the axles that came with the swap were really clean and in great shape. So i'm just thinking if a sway bar up front will stiffen it up so this doesnt happen or if it a problem that can become more serious.

 

sounds like axle bearings are going, grab the axles on the side where is comming from by the joints and shake it around and see if it moves. if it does, get a new axle.

 

I had a vibration problem under acceleration as well, it was my axles causing the problem, they were brand new but weren't balanced, I ended up buying new axles and put them in and my problem was solved, smooth acceleration again. Check your axles, I jacked my car up and hand spun the wheels and saw the shafts were looking like they were moving off center. I have a 99 civic as well and did a b18c1 swap, I was thinking at first that maybe I encounter some problem with the swap until I took a look at my axles, go figure brand new axles and they were both bad, then again I bought them from a dealer on ebay. Good luck