hmm, that's not good to hear. I'm surprised it wont run though, the old engine I had in mine was down on compression on cylinder 3, it was less than 90psi and it still ran ok, just breathed really heavily. I even did a track day with it like that and it ran ok, it used oil but was ok.
Does the misfire stay the same or get worse if you remove the plug lead from that cylinder? Are you sure the valves are sealing properly? Might be worth doing a leakdown test.