From looking at all your pictures you have come a long way since I stopped in here. Nice work!
PT base plates are definitely required. The post about cutting them out with a saws all is probably your best bet. Also the posts about doubling any vapor barrier is right on. Not to be done.
I didn't notice any drop ceiling mains or anything so I don't think you've installed any yet thats good. Like someone said that is done after the walls are up and I wait until the walls are painted also.
You're question about running the ceiling all the way to the wall in the areas where the duct work is close, I would. You will save allot of ceiling framing. If you loose headroom that could otherwise be used than don't. A few inches is nothing to worry about if it saves more framing.
You were prepared for a learning curve, you have found one in the base plates. Take em out and do it right. Never listen to a box store employee. You need to know what you need not someone else. Do your homework before going to the store. A lumber yard would have been a better place to order this much lumber and the assistance would have been better.
Great job I know your having fun. Wait till the rock goes up and you will really be excited!