I do think now the end is all c# dorian. Good stuff
You mean both solos?
Well, yes and no. Bayliss is much more wont to using entire scales instead of abbreviated scales such as the pentatonic. In this case he often highly stresses that #6 that is the character tone of the dorian scale whereas jake often plays more pentatonic like scales that do not have the 6th. This gives bayliss a more diverse sounds pallet but then jake takes over and brings the power with the rougher, yet more familiarity of pentatonic-ness. Its kinda weird but I hope that helps
Disclaimer: at work, no guitar in front of me, this is all coming from my fond memories of jamming along to this song many times. Haven't played 40's in a while, so don't hesitate to tell me I am totally wrong.
I think you are absolutely right on Brendan's solo; it seems to be Dorian with creative accenting of certain notes (definitely Bb, that would be the #6 you mention). However, when it switches over to Jake and the C#m, E, Ebm, F#m progression comes in, Jake occasionally throws in lines that seem to be C# Aeolian (regular minor), not Dorian. He throws in a normal A instead of Bb (which is the main difference between Dorian and Aeolian). It works because F#m has an A in it. If my memory serves me correctly, this is the note that Jake uses to get that dark characteristic to his solo, which C# dorian doesn't achieve over this progression.
I'll pick up the axe when I get home, but until then, feel free to check me on this. I think this is a case where it is a bad idea to overthink exactly what mode/scale to use. Jake's solo goes over a progression that allows for some creative tweaking of notes depending what chord of the progression you are on.