The oil pump on the FJR is seriously stout from what I've seen on a disassembled motor. It's an amazingly simple design (maybe by choice). It can take a ton of debris and throw it without failing - way more than the screen or the filter could pass. I'd be shocked if it has a problem. If it is not working correctly (not putting out enough oil pressure), and you have the oil level within the acceptable range, then the oil pressure sensor would be tripping a light on your dash. You would also be hearing very noisy valves, as these components are farthest away from the pump, and at the highest level (i.e. - lubricating those parts takes the highest amount of pressure). There could be other problems (bushing/bearing failure for example) whereby the pump is putting out pressure, but is starting to fail. In that context, surely you would be hearing some really bad noises or feeling some really bad vibrations.
OTOH - when you engine's oiling system is working right, and the engine is running, the oil pump is sucking oil through the filter and throwing it all over your engine. You valve train at the top of the engine is experiencing a Category 3 hurricane of oil, quite literally bathing everything in copious amounts of lubrication. The volume of that oil being used to lubricate your moving parts has to come from somewhere - that would be the sump of course. Naturally, this will lower the amount of oil in the sump, transferring that volume all over your engine, and thereby lower what you can see (if anything) in the sight glass.
To put this in perspective, on my bike, the difference between the "low" and "high" mark on the sight glass is about 1/2 a quart, give or take. On a 4 1/2 quart sump (give or take), that 1/2 quart represents about 11% of the total volume of oil in the engine. From the low mark, it would only take about 2 ounces for the oil to disappear entirely from the sight glass. Since I don't have x-ray vision, I have no idea exactly how low the oil in the sump is lowered past the end of the sight glass when it is running. But theoretically, it might only be around 15% of the total volume.
But I digress....
(ahem)
Agree with Iggy - ride more, stress less....