With a humanoid rig it doesn’t require all the bones. It looks like all the bones you need are assigned except for the head bone. You’ll need to manually select that bone and assign it to the head slow in the inspector. I cover the process a bit more in depth here: Humanoid Rig Setup
As far as the T pose I wouldn’t worry too much about it. Usually Unity likes to have the perfect T pose to make it easier to setup, but you can still configure the rig without it. As far as the shoulders, usually when a bone shows up red it’s because the orientation is off somehow. If it looks fine to you just try it as is then apply and click done.
