I just changed the crankcase and gear oil in both my Blur and the wife's Buddy this weekend. I ran into the same problem you're describing with the gear oil but found a nifty solution. I went down to the auto parts store and got four lengths of decreasing diameter silicone tubing. The largest fits into the opening in my everyday automotive funnel, and the successively smaller sizes fit snugly into each other. The little $0.50 funnel I have has a little tie-off hole, so I just used a piece of twine to tie the funnel off to the license plate. Then with four step-downs in tube size (plus the tubing is semi flexible so it makes a nice arc) I was able to pour out a measured amount of oil into the funnel and give it the ten minutes it needed to drain all the way in. Looking at the old oil, the shiny metal flake throughout was pretty alarming!
Change your gear oil people!
Another handy tip would be to drop by your local motorcycle shop and get a measuring cup. Use it to catch the old fluids as they drain. That way you can keep track of how much oil came out of your gearbox - as it's only supposed to have .100 L max in it. I was able to measure exactly how much came out and replace with exactly that same amount (about .09 L) so I know I'm not overfilling.
As for when to change oil filters, on the filter itself, it says it's good for 5000 km. There's no harm in changing it, but don't sweat it if you follow what the manual says. Swapping the oil itself has the greatest benefit to the engine, as whatever is caught up in the filter element is pretty likely to stay there. And if you're worried about when to change oil, I'd recommend switching to synthetic oil once you're well out of your break-in period. Synthetic has a lot longer life and doesn't go to sh__ as fast as it gets old.
Regarding air filters, an easy test is to pull the element out and hold it up to the sun. If you can see light clearly through it, hit it with compressed air from the back side and put it back in. Change it when it gets noticeably dirty because only then will it be making any real difference in airflow or performance. Like the oil filter, it's unlikely that any grit it's caught will come loose. I wouldn't do more than inspect it at oil changes. Unless you're up and down dirt roads all the time, changing the air filter that much is probably overkill. For what it's worth, the air filter on a lot of the old Vespas looks like a little cage of three layers of metal screen door. So the proper air filter in our scoots is a huge improvement. Keep an eye on it, but don't sweat it.
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