> Was it SP or UP who changed the track number designation from say Roseville to Emigrant Gap as being (CP TK 1) Track 2 and (SP TK 2) Track 1. Has it always been this way?

Some changes. #1 track between Coflax and Rocklin is still #1 track and #2 is #2. From Colfax to Sw 9 it hasn't changed either, unless you take into account a whole handful of short line relocations during the 1910-era double tracking project. From shed 47 to W Reno, the UP reversed the track numbers so that if you face east, #2 track is on the right -- this was done for the benefit of MofW personnel so they wouldn't get onto the wrong track to do their work (there had been some severe accidents in this respect over the previous 5 or so years).

> Did it have anything to do with the bi-directional signal project?

No. As of about 10 years ago, the long range plan was to CTC the entire Mountain and install universal crossovers at Verdi, Floriston, Midas, and Gold Run. I'm not sure how much of this has been accomplished since then.

> Does it make sense at all?

It's the UP's new mileposts which don't make sense, particularly west of Colfax on #1 track.