In case anyone else wants to take this alternative route, I'll post my experience.
Getting out of San Diego: I left downtown San Diego on a Friday morning in April by Market St (surprisingly quiet at 7.30 AM), Imperial Ave,Lisbon Rd, Jamacha Rd, Apple St, Maya St, Jamacha Blvd to join Hwy 94(Campo Rd) after Jamacha Junction at the big supermarket (Albertson's, I think).
Traffic: Going from not much to very little, especially east of the junction with Tecate Rd. Some places with broad shoulders. In general absolutely aggreeable surface.
Climbing: Gently rolling or slight climb as far as Dulzura, then you lose it all down to Barrett Junction, from where it is a long continuous climb to the Tecate junction and 1-2 miles beyond. Anything from there to Boulevard seems to be gently rolling.
Services: After Dulzura, where I stopped for an early lunch, nothing caught my attention until somewhere about Campo/Hacienda del Florasol/Barrett, where I noticed some small grocery stores. Not said that nothing was there, but I didn't notice, and Potrero and Canyon City in my memory seemed veeery quiet! Then the road runs a short distance through an Indian reservation, but the most obvious activity there was the school. From the junction with Old Hwy 80 shops and restaurants start coming back. There's a motel in Manzanita/Boulevard, where I stayed arriving about 4.30 PM.
I think there is a campground or two somewhere off the main road, and a motel in Jamul or Dulzura, but beyond there you'll have to go on Manzanita/Boulevard(Live Oak Springs is hardly on the way), if you don't carry a tent.
Conclusion: I haven't biked the official Southern Tier route, but judging from journals like "Fools on a Mission", the Hwy 94 must have less up-down-up-down and not traffic worth mentioning. The distance from San Diego to Boulevard is manageable, if you don't carry much stuff, are averagely fit, start early, are relatively lucky concerning breakdowns and the weather is friendly.
Beyond: I continued to Phoenix, mostly by the "unofficial" route. From Boulevard, it's downhill for 20 miles, until you enter the Imperial Valley (at first desert, then later, much later, irrigated groves and fields). Stop and eat at the café in Ocotillo, as anything edible between here and Calexico is roadkill.
Hwy 98 is quiet, straight and with a great surface. The grocery stores at Bond's Corner has been boarded up a long time ago, so stock up in Calexico, where there are also plenty of accommodation.
After you join Interstate 8 and parrallel roads (I really hope they'll condemn the Evan Hughes Highway, or else redo the surface. It's a really bumpy ride. Riding on the Interstate where there is an alternative, however bad it's in, is illegal in California, but concerning traffic it's perfectly safe, because there is very little)the only service until Yuma is an RV park a few miles west of Gordon's Well. Next to it is what appears to be a restaurant, but it was fenced off, and there was absolutely no activity that particular Sunday afternoon.
In Yuma you enter Arizona, and you are then allowed to bike on the Interstate when you're outside of cities with 50.000 inhabitants or less.I'd advise people to rejoin the old Hwy 80 at Ligurta (traffic is even scarcer than on the Interstate) because the surface is good, and the Interstate shoulder has a lot of rocks lying on the shoulder (yes, I did have a flat tire..!). There are motels in Wellton and, more conveniently, Tacna.
10-15 miles out of Tacna, US 80 merges with I8 about where the irrigation and human activity ends.
Even if staying in Tacna, the next day trip for non-campers will be long (70 miles or so). There doesn't seem to be any accommodation between here and Gila Bend. At Dateland there's a restaurant (with the famous date icecreamshakes), but no longer a motel. The only road for of the way is I8. Still not with much traffic. Landscape: Desert, and more of it.
Phoenix can be made in one more longish day trip. If you go north to Buckeye, you will get built-up areas and choices of accomodation quicker than going east to Maricopa (across the Indian reservation and south of South Mountain), but I suppose it depends on where you are going in Phoenix. The only time I felt disturbed and discouraged by traffic was on the last strech of Buckeye Road going into Phoenix, where the road was busy and the 4 tracks were so skinny that the trucks could hardly pass me. Soon as sidewalk appeared, I rode on that. There are probably lots of quieter alternatives to Buckeye Road, but I was to lazy to explore them.
Thus San Diego to Phoenix can be done in a 6 day trip, but you are pretty stuck with distances 40 to 70+ miles a day if you won't (wild) camp.