Ozzie
Presuem you have the answer to the clutch housing hole?
In case not, it's there to let any minor oil leaks out rather than contaminating the clutch plate. If you plan on goign through deep water, you should put a wading plug in it (essentially a threaded sump plug) to stop water getting in.
You'll have a second similar hole further forward at the front of the engine too.
re: gearbox - you really need to pm jamesmartin - he's the man when it comes to gearboxes.
Sam is probably right, but I don't know enough to be sure. Gears have a syncromesh ring which matches the speed the gears are turning to each other to avoid them 'clashing' and to make gear change easy.
If one of these rings is failing, could explain your problem.
Might be worth changing the gearbox fluid (MTF 94 or Automatic Transmission Fluid Dex II or III - don't even think of putting EP90 in it!!!) to see if that improves.
Also see whether double declutching when changing into 2nd helps - if it does, would support it being the syncromesh. Google search on how to double declutch if new to you, but in short this means declutching, shifting into neutral, re-engaging the clutch, maybe rev-up the engine by dabbing the accelerator in between ("midway throttle"), and than de-clutch again and shift into the appropriate gear.