1) Replace all the bushings in the shift linkage.
2) Adjust freeplay on the clutch. Oftimes with a problem such as yours, if a clutch is not engagine/disengaging completly the heat produced during driving will cause all parts to slightly expand which, in turn, makes it difficult to engage/disengage the lower gears. This would be particularly noticable when trying to engage first gear following neutral when the dragging clutch keeps everything spinning while you are attempting to make a silent entry.