You would need to provide a whole lot more info than lots of shoulders in order to give some reasonable recommendations. For instance, I "assume" you are camping and prepared to cook your own food (as opposed to eating all meals in a cafe). How far can you ride a day fully loaded. How often will you realistically take a rest day? Will you do rail trails with a fine gravel (screenings) surface or must it be paved). How much traffic can you tolerate without a shoulder, i.e. 1,000 cars a day? What time of year are you planning to ride? What type of scenery do you like, i.e. mountains, farmland, wide open country. Give some guidance and I (and others too I am sure) would give some suggestions.
Honestly, if you got the time, I would highly recommend you take the TransAm route (1st choice) or the NT (2nd choice) or better yet, a combination of routes (best choice). Except for getting out of Portland greater area, you really should not have that much trouble with traffic. Remember, THOUSANDS to TENS of THOUSANDS of riders have done these routes and there are very few fatalities. I have done 50k+ miles of loaded touring over 35 years and the TransAm is still one of my favorite routes. Sure you will have certain "traffic issue" areas but the routes is 4k+ miles long.
I understand your concern about traffic along the SC route. Remember though it is trying to follow a specific pre-existing route so they were/are limited on were to go. I too personally would not enjoy riding this section. If you want cars to give you more space, consider installing a "safety wing" such as this one http://www.cantitoeroad.com/accessories/safety-wing
. I personally do not use one but have seen some cyclotourists who do and they swear by them. You might need to be creative in the mounting if the packs get in the way.
If you currently are riding in the Portland on the road, you should be fine doing most ACA routes.