I had the same issue it vibrated a lot, I joking referred to having a shaker spoiler due to the vibrations, I thought it was the balance shaft I disabled w/ poly mounts as well, after spinning a bearing in under 45 miles, I had the engine balanced before rebuilding. The flywheel was out 70 grams, now its back together and I put the balance shaft gear back in, I can set a glass of water on top and it only oscillates slightly at idle.
I thought I should mention, yes I had the flywheel ground and balanced, by a vendor on here that is no longer with us... for obvious reasons.
[This message has been edited by 86GTFastback (edited 01-16-2014).]