Starting on a review:
I'm arbitrarily starting in the middle of your comments, as I catch up on this now I'm back from Florida. Keep your other comments coming, while I catch up.
7: NinaLeeRd -> CarrRd
Leaving this alone. Carr Road seems to be discontinuous, thanks to the new port of entry, with Nina Lee a separate road helping to connect the two parts of Carr Rd., with signage at the interchange pointing travelers to Carr Rd. rather than identifying the bridge as part of Carr Rd. Anyway, NinaLeeRd is a point in use, would rather not disturb it.
9: MillSt -> GlenArbRd (more important)
Will do.
11: CA125/905 -> 1A?
Exit numbering is confusing, with 1A used for CA 11 EB to CA 125, and for CA 11 WB bypass ramp to La Media Rd. (CA 905 exit 7), while 1B is used for both CA 11 EB to Enrico Fermi Rd. and CA 11 WB to CA 125. Leaving this alone for now, maybe the exit numbering will be cleaned up once CA 11 is extended to a planned new border crossing.
12: FreDr is just westbound 12, so these waypoints should be deleted
Caltrans' Postmile Query Tool disagrees, putting CA 12 on the routing shown in the HB at this iunctiion, and identifying the one-way Fremont Dr. connector as not state-maintained. This also comports with my field-check of this junction.
12: CA121 -> CA121_S
12: CA29 -> CA29_S
The CA29/121 waypoint makes it unnecessary to add directional suffixes to the other junctions of CA 12 with CA 29 and CA 121.
12: I-80(40A) has been moved east
In my local copies of the CA 12 and I-80 files. The relocated point is only 0.06 mile from 40B. But the HB now treats them as separate interchanges (40A with Green Valley/Lopes, 40B only with I-680) -- they once were combined into a single interchange -- and I would keep that as is.
12: PotRd -> GlaRd; shift west to the overpass?
Point renamed, but not relocated.
Other CA 12 changes not otherwise discussed are in my local copy.
13: should 1B be added? it's not exactly the same interchange as 1A
13: I-80 -> I-80/580
1B really is part of the 1A interchange, connecting CA 13 to I-580 WB and from I-580 EB.
The other change will go into my local copy.
14: CA14Trk -> I-5Trk; ca.ca014trknew is an I-5 truck route
14: CA178_S -> CA178_W, CA178_N -> CA178_E
Going into my local copy. The new I-5TrkNew file will be added later.