If you left the WIR and ensuite where they are you could put an obscured window in the WIR for natural light. You don't have any plumbing in the wall between ensuite and bed 2 so may not be as bad as you think if you put noiseline gib and insulation in that wall (but I'm no expert).
I think I'd switch the shower and vanity positions in the ensuite so the plumbing for the shower isn't in the wall right by your head.
As a potential money saving option, do you need the cavity slider into the WIR? I bet you'll never close it.
Is it in the budget to get a bed-frame that has builtin shelves in the headboard. Since you don't have space in the master for bedside tables you might want to think about something like this: