Harry, thanks for posting these photos. Brings back pleasant some memories of youth in Marin. It's wonderful that SMART is now developing bicycle trails along the old NWP right of way, in conjunction with rebuilding the NWP San Rafael branch.
As a kid, growing up in the Terra Linda area during the sixties, I often rode my bicycle over Puerto Suello hill to visit San Rafael. In those days, there weren't bicycle paths, lanes or bicycle friendly places that Marin has today; just the highway over the hill. Thus, I would cycle along the margin of Highway 101 for a few hundred feet to reach a freeway exit at Lincoln Avenue, much too close to speeding autos for comfort or safety. After the NWP's Puerto Suello tunnel no. 4 was rebuilt from the '61 fire-collapse and re-opened to rail traffic in '66, I once braved cycling through the tunnel as a short cut to avoid the highway. Thinking ahead as to what I could do if a train came into the tunnel, I observed its smooth concrete walls didn't provide much refuge. Never again went that way.

Bill, I observe that the gradient on both sides of Puerto Suello tunnel exceeds 1%, and trains often worked hard in both directions. According to Fred Stindt's excellent book, "The Northwestern Pacific Railroad", vol 3, the elevation at San Rafael, MP 17.0, is 5 feet; at Glen Park-Grand Avenue, MP 18.1 (south end of tunnel along Lincon Avenue) is 105 feet. The elevation at Cerro, MP 18.7 (north end of tunnel) is 72 feet, and at Forbes, MP 19.6 (Hwy 101 and SMART's Civic Center station) is 12 feet.
Putting those numbers into a calculator yields 1.7% and 1.3% at south and north approaches to tunnel 4, respectively. These are averages - a profile chart may reveal short sections up to 2% gradient. Although before my time, there are historical accounts of steam helpers assisting northbound trains from San Rafael up to the apex at tunnel 4.
During the early seventies, NWP regularly ran a turn from Healdsburg to San Rafael on weekday evenings, usually consisting of a single SD-9 lugging a dozen or so aggregate hopper cars. The "Gravel Train" usually passed my mobile home park at Gallinas slough with southbound loads about 7:30 PM, and returned northbound with empties about 9:00 PM. Although I was 2 miles as the crow flies from Puerto Suello, on windless evenings I could hear that SD-9 thrum up the grade in both directions, go silent as it entered the tunnel and then faintly hear it emerging on the other side. Music to my ears (but not my neighbors and residents of the area)!