I've no experience with the AT so this is generally for carbed bikes.
As a rough rule of thumb you loose 10% power every 1000m (3000ft) with a healthy engine This means that you should loose approx 5% at 1500 ft, and that's "nothing".
The reason why you loose power is that your air/fuel-mixture gets fatter (less air for the same amount of petrol). As you mention it's possible to remove the airfilter to get more air, but it's usually not smart in the long run.
Another option is to remove the snorkels on the dirty side of the airfilter (if AT have snorkels), or modify the dirty side (drill holes etc).
The other option is to reduce the amount of petrol. You can do this by smaller main-jets and/or drop the needle.
Remember that running fat is not dangerous for the engine, but running lean can be very dangerous. So if you do a modification you have to restore it to original state before you get to a lower elevation.
If you have enough power there is nothing wrong to keep on driving like it is now.
The Remus itself usually make the bike run leaner (which should help you) but it's possible that jets/needleposition where changed at the same time to compensate for this. Maybe it's overcompensated. If the carbs are worn they also make the engine rune rich. Do you have a dyno-kit? They suck.... A dirty airfilter will also make the engine run fatter.
I would have done a testride (a few 100 meters) without the airfilter to see if it gets better.
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