In a former life, I worked for Team Warlock. I'd help tune the boats for the high elevation poker runs in Sac and Lake Tahoe. I know, dream job, but everyone has to eat, right?
Anyway, at 5000' ASL, you should be very rich. You will need to jet way down and adjust the choke set up as well. You went the wrong way with the jets. I'd try 32 for the pilots (may still be rich) start with taking two steps down on the mains.
Another root source of the symptoms you mention could be vacuum leaks. Hard to tell without the bike.
As a side note: at 5000+ elevation, expect a 20% or more power loss across the board. Dropping a tooth in the gearing will help restore some of the performance loss. We would drop 4-5 degrees in prop pitch when running elevations.
