I can't give you specific jetting, but here's some guidelines and resources:
www.hondaxr.com has correction factor tables, which account for altitude , temp. and airbox/exhaust changes.
To my surprise, my local dealer (who installs a lot of XR 400 big bore kits) told me that the bigger bore doesn't need much larger jets, if any. They recommend going up one size on the pilot (slow) and main jets.
According to Supertrapp, 4-6 discs creates about the same backpressure as stock pipes on later model XRs (not sure about your year). I notice a lot of guys run 12, which frees up exhaust, improves top-end and affects jetting (go a little richer on the main). Although, fewer is quieter, which is important too.
You should probably jet for your leanest condition, which means jet for sea level. You'll be rich at 5000'.
Given the above, you might need to increase the pilot and main one size. If you opened your airbox and exhaust, it would be more likely.
When I change altitudes, I switch between a K&N (higher altitudes) and the stock air filter (lower altitudes). This seems to help a little and avoids jet changes.