I spend a lot of time up there, we have a house in Healdsburg (which we rent out by the way, but we have a 3 night minimum).
First off, I would say "screw Napa". The cycling in Napa sucks
If you do end up in Napa, I would recommend that the only way from Napa to Sonoma that you use is 128 north from Calistoga or Mark West Springs The southern crossing is very much not fun (traffic). Oakville Grade and Spring Mountain Road are extremely difficult climbs. I rode from Healdsburg to Calistoga and back this weekend, there is one small climb just North of Calistoga but it's not difficult.
One possibility. Start in Petaluma. Bodega, Valley Ford, Valley Ford Freestone, Bodega, Bohemian, River, Sunset, Westside, stay in Healdsburg
Day 2. North out of Healdsburg on Healdsburg Ave, Lytton Station, Alexander Valley, left on 128, right on Geysers, right on Red Winery (this is an extra loop well worth taking), Pine Flat, left on Alexander Valley, 128 into Calistoga, get on Silverado, stay somewhere in St Helena.
Day 3. Head South on Silverado to Napa. Double back after checking out Napa (Silverado is a decent road to do twice). In Calistoga again, take Petrified Forest off 128 and then right on Franz Valley School. Left on Franz Valley. Left on Porter Creek and then onto Mark West Springs. This road is more trafficked than anything so far, but it's not too bad and there is a downhill. Cross 101, left on Fulton. Left on 3rd into downtown Santa Rosa. Some urbanish cycling but good bike lanes. Right on Brookwood, left on Sonoma. Right on Yulupa, turns into Bennett Valley. Right on Grange. Left on Petaluma Hill to Petaluma.
If you want to include roads like King's Ridge they will be much harder and you probably won't be able to include a Napa leg. I'd recommend this, if you are interested I can design something there as well. Don't pick Skaggs Springs Road or Fort Ross unless you are extremely fit.