Once a santro, owned by my company needed new clutch plates. they wanted to sell it. anyhow now clutch plates were installed. and this same problem came. with normal race, it gave jerks. but with high race, it was fine. so it is a confirm problem of clutch alignment. it was surely mistake of mechanic. for your problem to me it seems that it is clutch work. when is last time u replaced it? what is model and mileage?
mostly if u remove engine and transmission for any problem, be it plates, bearing or fixation, it is a good idea to replace clutch set. in this process mounts if broken will be replaced, all nets screws tightened, bushes replaced hopefully everything will be fine. u just need a mechanic who can do it carefully.