The secondary U-detent is not required. I have a 90's Benchmade CQC-7 (970) and it does not have the U-detent. The lockbar appears to be the only detent. It has a much larger washer on the presentation side that centers the blade and it does a great job at it. I'll bet this is what was done on early CQC6's as well.
Cutting the lockbar would require a water-jet cutter or laser, but seeing your work I'll bet you could pull it off with hand tools/dremel and fine cutting wheels. It would be fine for a 1-off project, but a pain if you decide to make more than one. I know I could do this, as I've made cuts like this in Ti for other applications and it works just fine.
Pressing the detent ball is easy enough provided you get sizing spot on, and for the ball you just need to source small ball bearings. Not sure from where, but I've seen them in my various mechanical fuk-ups when they go bouncing across the floor into the dimension of lost keys and single socks, so I know they're out there if you buy a particular bearing and pry the races apart. Off the top of my head R/C car bearings might be a good source.
Detent hole on blade is easy. Assuming you go with a solo lockbar detent, just drill the detent hole on the lockbar and do a mock assembly with no scales and no detent ball installed, then close the blade and you can mark the blade for the detent hole through the lockbar hole. If you are using a blade with an existing detent hole that gets in the way of function I'd just do a quick spot weld on a low setting and grind it out for a clean surface. That shouldn't change the properties of the blade steel in any way that matters ...?
If you make your own blade I vote Damascus!
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Edit to add: if anyone from EKI is reading this I promise not to make a 6 if you sell me one. Otherwise I'm probably going to do it when my gun projects are completed and my boredom level reaches a certain point. We get a lot of rain here so boredom level goes up fast...