I'm not familiar with the KLR specifically. Hopefully the bottom end is as robust as mentioned.
Problems at altitude suggest lean fueling and over-heating and this can lead to engine damage. If the cover has blown off something has forced it off.
As a first test: Inspect the valves mechanisism with the rocker covers removed. Then check does the engine turn over. By hand; don't press the starter. If you don't have a socket to put on the crankshaft,take out the spark plug(s), put the bike in second gear and turn the back wheel. Is it seized?, making odd metallic noises?
How did you top-up the oil? I'm puzzled by "oil part of the cylinder" comment. How much oil did it need?
A few photos of the top-end might be useful - but that will only satisfy my curiosity . I think you'll need some expert mechanic to investigate.
Buena suerte
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