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The other day I noticed that the cap on the gearbox oil filler was open... and just above there has clearly been coolant loss.... I was a bit concerned that water could have gone into the gearbox. Further to this I wondered how I can check to see if the gearbox has sufficient oil... is there a way to know?

Also when I removed the air cleaner from the throttle body, I had to also remove a black rubber pipe from the air clearer housing, I was really concerned to find the tube full of light brown sludge. I can't see where the pipe goes to but it has a small filter on the inlet to the air cleaner.... can anyone shed any light on this please?

I believe the geabox has a yellow plug at the top of it, which you can dip your finger in to check the oil level.

As for the pipe you're talking about it's the 'breather pipe'. You can either detach it and fit a tiny breather filter on the end OR keep it standard. As long as there isn't too much sludge blocking the entire pipe there isn't anything to worry about. It allows ventilation smoke from the bottom of your engine to return into the system via your TB.