"The room can totally wreck, or make, a system"

Design, including how the space is built, solid, laid out well, etc do the best you can then work around the other uses of the space. This will determine where the speakers are going to be generally located so pretty easy to sort out where the main treatments will be needed the most. The better the design of the space, the easier everything else will be.

If a room is to far compromised then all the treatments one could do might not be enough. I have listened to very high end systems I had to walk away from they sounded so bad yet I have enjoyed simple but well sorted systems what were a joy to listen to.

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40 hz null pretty tough to deal with

90 hz peak, I would look into a trap(s) tuned for 90 hz

Peaks are far worse to listen to than nulls and often easier to fix.

Room treatment is my second most expensive component. 

Room treatments can only get you so far.  In my experience, DSP-based room correction was needed to bring audio bliss to my systems.  My hunch is that pending money on DSP is likely going to by more cost effective than room treatments as a primary solution.

@fynnegan  I had a similar issue 50hz to 100hz…Applied room treatment, bass traps & absorption panels, only thing that corrected the problem was changing out my speakers to a set of Soundfield Audio MMW-1’s Cardioid Stand mounts with built in active front & Top Firing Subs controlled with DSP. If you don’t know what a Cardioid Speaker is Google it, it’ll certainly apply to your situation.  I opted to have my set built with Beryllium Tweeters and I have to tell you, In the past 5 years I’ve gone through 11 sets of speakers going nuts trying to correct the freq bump in the room. These are number 12 and they’re absolutely amazing and in combination with my room treatments the bass issue has totally been corrected and am finally off the speaker merry go round and finally enjoying my music!

I just got back from the Florida Hifi Expo in Tampa, I gotta tell ya, I seriously felt my set up sounded as good if not better than many of the High End systems I saw. I went specifically to stop by the Soundfield Audio’s room just to thank AJ, the owner of Soundfield Audio, for finally getting my room sounding right… and here’s the kicker, No Lie… His room was prob one of the best sounding rooms at the show and when I told him that he said he’s been hearing that all day. 
So yes DSP at this point may be your only option as it was for me and combine that with a quality speaker custom made for your tastes and room’s needs and I can assure you,  you’ll never look back !