Jeff - Having read and reread your post. A couple of things spring to mind and are worth mentioning.
I ride at about 1000metres usually - but when I travel to the coast - well it's at sea level. So I do understand. Also played a lot in the Austrian Alps as a youth and have seen what happens when air supply drops too far.
90% of the TuneECU maps you'll find are liable to give you trouble (from experience). They'll be way too rich for 3000m.
Many will be made for power and concentrating on the Fuel Tables which are TPS based, whereas given your altitude variations and type of riding - I think you'll be needing well adjusted L tables. The L tables are manifold pressure based.
This is - from experience - not that easy. Sadly! - I wish it were.
Allow me to suggest considering a Power Commander 5 with Auto/Tune. Have the bike tuned properly at whatever altitude. And let the PC5-AT do the altitude O2 adaption for you. You can also use a PC5AT in pressure mode - but whilst it is excellent you will spend many many not so fun hours trying to get it right.
This was a marvelous thread started by one of our more OCD tuning chaps
@Claviger - I took the bull by the horns and had a go with his help, but boy was it a job. Nevertheless - have a read
How To: Add Pressure Input for PC-V