You cannot immediately check the oil volume accurately after running the engine; you must wait for the oil to drain from the engine passages into the sump for an accurate indication in the sight glass of the crankcase oil level, indicating its volume.
How much oil did it take to "fill it up," after you stopped?
Keep an eye on the oil level (after the lubricant has had time to settle in the sump) and your mileage vs. how much oil is needed to top off the level to the higher sight glass mark.
Possibly, you have a non-problem, with nominal oil mileage. Worst case: You have one of the unfortunate '08-'09 KLR650s with an excessive oil appetite. If the latter, replacement piston and rings is in order, based upon the reported experiences of other victims of oil-hungry '08-'09 KLR650s.
Further worse case: If the engine suffered oil starvation during its service life, chances are the exhaust cam journals, cam caps, and the exhaust cam, are TOAST. If so, you'll need a replacement cylinder head (cam bearing surfaces are integrally machined), cam caps (uniquely machined with their head), and exhaust camshaft (intake camshaft probably can be salvaged). An alternate fix is an involved and expensive rehabilitation of the head, and some new parts.
Unfortunately, you did not inform me early enough about your stripped oil drain hole, so I could have suggested an OVERSIZE OIL DRAIN PLUG, instead of the insert!