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