It looks like you have a good start with equipment. I’m not sure why you would upgrade the Onkyo as it seems like it would do everything you need it to do. I’d take the money you were going to spend on the Denon and put it into room treatments.
I would sell the Klipsch sub and get another Hsu. Having one sub that is so much better than the other will not help you.
Is this going to be for a dedicated theater or multiuse room? Projector?
It looks like the room is open to the rest of the upstairs and just has a handrail around the staircase. Light and sound control will be difficult with that setup, but sometimes you have to work around such things. Are you building a riser for the second row of seating?
7.1.4 Theater Room (In Progress): JVC-RS46U, Silver Ticket AT 2.35:1 142”, Onkyo RZ830, Anthem PVA-7, Panasonic DBT-110, JBL Studio 270’s, 4 - 15" DIY Sealed Subs
3.1 Living Room: Samsung 64” F8500 Plasma, Anthem MRX 300, Dynaudio Audience 52’s, Dynaudio Audience 122C, NHT SubOne