Excited to see your progress! Even though the KA24DE is a bit dated, I honestly think they remain heavily underrated. So many people moved away from them to the SR20, but the KA is (at least in my opinion) much more stout, and it's hard to turn down so much extra displacement. It would be my choice of affordable swap if I was in a 510 wagon which I've always wanted. Even the sohc version in my D21 has proven pretty great, though it's now relegated to farm truck in mexico with my parents.
It's interesting that you didn't like the CD009, with how popular it is. Though I know most people have to swap shifters which affects how it feels a lot. I really liked the later JK in my G37s when I had that. Synchros were great, and the stock shifter felt "short enough" to not want to change anything. I hate short shifters and the notchiness, however. On my 71c trans I'm switching to the stock shifter housing and a nismo solid shifter. Throw will be a bit longer, but I want a slightly closer to stock feel and to not feel like I'm screwing up my synchros from a too-short and notchy shifter.
Also, surprised you got such terrible mileage on the 2JZ. What was your rear end ratio? My L28ET gets me 22-23 highway mpg when I've done roadtrips and it's not even really particularly well tuned for it. I've been tempted to switch from my current 3.9 rear to a 3.7 - the 3.54 seems a bit too long for my taste, but I think just swapping to the 3.7 might get me to an easy 25mpg with better tuning.