Alex,
If you have your gearbox in pieces, check that the screws in the figure '8' plate that retains the bearings are tight. With these screws loose, the shafts can creep forward, making the engagement of 2nd gear a bit shallow. At this point, it is a good idea to do a dummy build just to check that all gears engage by approximately the same amount. If 2nd is a bit shallow but 3rd is deeper, there may be some advantage in grinding a small amount from the layshaft where it abuts the rear bearing - this will move the layshaft back and increase the mesh on 2nd. When finally rebuilding the 'box, shim up the front of the layshaft so that the front bearing takes the thrust rather than relying on the figure '8' plate. Similarly, if top gear is a bit shallow, a shim behind the sleeve gear bearing will give more engagement - unfortunately, this requires complete dismantling of the sleeve gear assembly to insert the shim at the back of the bearing housing (and a similar thickness shim will be required behind the square bearing retaining plate, as the outer sleeve of the bearing will now protrude a little).
Unless the selector pins are very worn, they don't have much effect on the engagement of the gears - there is usually a narrow unworn area between the 2 worn flats, and this is the bit that registers in the camplate when a gear is selected - the worn areas only contact the camplate during changes from one gear to another. If you do find it necessary to have the pins welded up, make sure they are allowed to cool naturally - quenching will result in them being glass hard and snapping off in use.
Hope this helps,
Regards,
Eddie.