Although I have ridden cross-country more than a half dozen times, I have never done a complete ACA route. I don't mind doing parts of them - but I feel no obligation to stick to any predesignated route. I've done parts of the TA and did the much of the western section of the NT in 2006.
To answer your questions in the order listed:
1. The Hwy 20 causeway is busy but there is a separated bike lane on the bridge and a wide shoulder elsewhere. Remember, there is a great bike trail that goes across the bay from Anacortes. Also, you should really consider heading out to one of the San Juan islands as a delicious extra - I'm guessing the start of your trip.
2. Hwy 200 near Sandpoint is busy with very little shoulder. I rode it on my frist cross-country trip in 1987 and the difference is night and day. Still, Sandpoint has turned into a recreation-based community and most drivers are used to cyclists. Perhaps avoid the busiest commute times.
3. Logging trucks - not that frequent - don't listen to music while riding - you can hear them coming a mile away. But do given them plenty of room - they do move quickly .
4. US 93 north of Whitefish sucks - narrow, no shoulders, busy. There is a paved alterate - Fisher Creek & Wolf Prairie Roads - that have very low traffic and bypass Eureka thru the tiny community of Trego, but they still put you out on US 93. Or you can take Fisher Creek Rd down to US 2 - but US 2 has some of the same traffic and shoulderless issues that US 93 does. There is a fairly directly line unpaved road over the divide from Fisher Creek to Star Meadow Road via Twin Bridges Rd to Spencer Lake - - but still you have a short, bad stretch of US 93. I am amazed that US 93 has no shoulder right up to the edge of Whitefish - considering that Whitefish is such a recreation-based community - but Montana is the poorest state in the West. Also - in addition to a lack of shoulder, US 93's pavement is broken at the edge forcing you further into traffic. I have ridden 100,000+ miles and this is one of the worst mapped stretches - but as you can see, there are no alternates.
5&6. Going to the Sun Road is not to be missed. It is one of the finest rides in North America. Headin west to east the park has limitations on cyclists. The stretch from Apgar to Lake MacDonald Lodge is closed from 11a to 4p as is the uphill stretch from the bottom to Logan Pass. Leave early and enjoy the view with light traffic. I prefer camping at Avalanche rather than Sprague Creek - the former is quiet and gives you a head-start on the climb. The latter has close access to facilities at the lodge, but is right next to the road and has road sounds all night. One option you can consider - if you are not morally opposed - is to take all your gear up to the top on the free bus and put it in the lockers there - then ride up with a nearly bare bike. If you give yourself 3 hours for the climb you will have plenty of time. Then you should plan on spending a few hours up top hiking - if the weather is good. And it is unforgettable - the Highline Trail has eye-popping views and sheer walls.
7. US 2 does have heavier than ideal traffic - it has been widened in most of eastern Montana - but there are a few stretches where there is no shoulder and fairly heavy traffic - like east of Havre. I suggest taking US 89 southeast from Glacier to Great Falls - then US 87 and Hwys 80 & 81 to Hwy 200 across eastern Montana - mostly the L&C routing - but staying on Hwy 200 the entire way and NOT heading into Williston, ND.
7A. I would ABSOLUTELY avoid Williston. There is a huge oil and gas development going on there with industrial traffic and rowdy, impatient, possibly drunk, over-paid young guys in profusion. Cheesy motel rooms go for $200 a night if you can find one. I would stay on Hwy 200 to Washburn which has great Lewis and Clark and Mandan historic sites. There will be places on Hwy 200 in western ND that have moderate and moderate-plus traffic - but it is generally better than US 2. Hwy 1804 was named for the year Lewis & Clark went up river as a scenic road and was never designed for industrial traffic. I would avoid it.
If you are willing to make small alterations to the route - and ACA is working on publishing a North Dakota alternate right now - then you will have no problem.