Yeah, mine suffered at these altitudes too. Others have been fine though, so it seems luck of the draw.
The slide needles on early Transalps are not adjustable unfortunately. I suspect this is the case on yours too, but I am not sure about this.
You can change the jets though. At 5,000 metres plus, look to reduce the size by 10 to 15 per cent. Just make sure that you change back to stock as you come down. They are real small, so cost nothing in shipping. This will help a bit.
I am assuming you have done everything to free up the airflow into the filter yeah? Drilling holes is an option. You can tape them up later.
Around the world 2000-2004, on a 1993 Honda Transalp