Gear selection problems

Hello all, never been on a forum before so if I mess up a bit just bear with me! I have recently fitted a Maney belt drive and a set of RGM close ratio gears with new bushes, bearings etc to a gearbox bought off ebay. The problem I have is in down shifting,fourth to third ok,third to second hit and miss, second to first very difficult, incidentaly this box came with a reverse cam plate which I have used. I have rearsets and a norvil type gear lever set up i.e. linkage type, which worked ok on my other box. I have fitted spherical joint to the linkage rod and taken excessive freeplay out of footrest/linkage pivot with braze. What I am wondering is would the fact that the gearbox is now spinning faster cause a problem till the box is run in,or is it something to do with machining tolerances in the new gears-I had to do a bit of work to the mainshaft first gear to get it to fit on the splines,it was still a little tight but went on all the way ( without hitting it with a hammer before you ask!) all the other gears were sliding ok without too much fettling. Incidentally the clutch is clearing and not dragging. I am just curious to find out if anyone else has encountered similar probs.