From some of my own research, some of Joel Windmiller's, as well as from having seen Historic US 40 signs on some of these routes:
Starting outside of Vacaville, going northeast:
Midway Road east through Batavia
Porter Street northeast towards Dixon and into town
North Adams Street through Dixon to Route 113, OR "Old State Highway"/Porter Road to A Street, then A Street two blocks to Route 113
Route 113/First Street north to I-80
I THINK, but am not certain that Milk Farm Road is a later bypass routing before I-80 was built (it is named for the long-defunct restaurant there)- the original routing from there was...
Currey Road north to Sievers Road
Sievers Road east to Pedrick Road
Pedrick Road north to Russell Boulevard
(When Russell crosses over Route 113, that is where US 99W historically began its co-routing east towards Sacramento)
Russell Boulevard from there east into downtown Davis at B Street
B Street south to First Street
First Street east to Richards Boulevard
Richards Boulevard southeast under the railroad tracks to Olive Drive, a block from I-80
Olive Drive east to where it dead-ends at the I-80 ramp
The original US 40/99E through East Davis then is subsumed by I-80 until the intersection of Road 32A and 2nd Street, at which point Road 32A east to I-80 at the Yolo Causeway is the original US 40/99E (with the original pavement)
Between I-80 Exit 78 (Road 32A) and I-80 Exit 81 (West Capitol Avenue), the original US 40/99E bridge is long gone, but ran to the north of the current I-80 structure
From I-80 Exit 81 east, US 40 used West Capitol Avenue through West Sacramento and then the Tower Bridge and Capitol Mall to reach downtown Sacramento. (In the 1950s, what is now I-80 from Exit 81 to the 80/50 split, US 50/Business 80 to the Downtown Sacramento exit, and what was once Route 275 via the Downtown Sacramento exit to the Tower Bridge was US 40/US 99E, both later co-signed with I-80 if I am not mistaken.)
US 40 in Sacramento itself actually had the fewest alignment changes through the downtown area, usually continuing around the State Capitol via the one-way pair of L and N Streets from 10th Street east, to 16th Street, then heading north via 16th Street to the current Route 160 bridge across the American River. (At 16th Street, US 99W and US 99E merged, with 99E starting co-routed with US 40 north). In the 1950s, the 12th Street/F Street/15th Street southbound segment was introduced to provide a one-way pair for this portion of US 40 and US 99E.
(In the 1960s, briefly, US 40 and US 99W switched over to 3rd/5th Street and P/Q Street to get to 15th and 16th; there's some 1960s BGSes remaining across from Fremont Park at 16th and P as a result.)
After leaving the edges of downtown Sacramento, US 40 originally made shoreline at what is now the Northgate Boulevard ramp, and followed Del Paso Boulevard northeast. This was bypassed in the late 1940s by the current Del Paso Boulevard left exit (I'm not sure if this occurred before the North Sacramento Freeway, today's Route 160 and then Business 80 from Arden Fair northeast to the Marconi Curve, was finished).
Through North Sacramento, US 40 followed Del Paso Boulevard northeast to El Camino Avenue, then went east along El Camino Avenue to a now-removed intersection with Auburn Boulevard; originally, the intersection was configured so that through traffic would not contiue straight into Arden-Arcade via El Camino, but instead through to Auburn Boulevard northeast.
US 40 (and 99E) followed Auburn Boulevard all the way to Roseville from that point; however, thanks to the construction of the US 40/99E freeway (later I-80, now Business 80) in the area, the westernmost segment of Auburn Boulevard (from El Camino to Marconi) no longer connects to the longer segment from Marconi Avenue northeast to Roseville.
In Roseville, Auburn Boulevard becomes Riverside Avenue (which carries US 40 into the old town area), then Vernon Street and Atlantic Street. From Atlantic Street, US 40 then follows Taylor Road/Pacific Street through Rocklin, and then Ophir Road back to I-80 near Auburn.