If the shifter cables are fine and bolted correctly then I would see about it being the TOB (throw out bearing) which is on the shaft inside the transmission which works on the fork the slave cylinder pushes. If that were to come loose or off in those effects it may do what your talking about (noises and such). Someone correct me if I'm wrong but this happened to me before and maybe I'm not wording it right.

You may also want to try Club3G since its more related to your style of generation car and you might get a faster answer that way. Just a suggestion if you haven't done so already.