Here is my take:
Don’t buy a “custom shop” thinking it is a higher quality/trim level. A Custom Select is the same trim level/quality as a Select. Only difference, you get to choose the options on a Custom Select where a Select is a stock configuration.
Masterbuilt is a different deal. They are not taking Masterbuilt orders from the general public, so at the moment talking USA “custom shop” versus USA production is a conversation of Custom Select vs Select.
The main reason to go Custom Select “custom shop” IMO, is to configure the instrument exactly the way you want it.
IMO to pay new custom select prices for a model that a dealer spec’d and listed defies the idea behind getting a “custom shop” instrument that is crafted to your personal preferences. You are really paying about a $1,000 premium to get the “Custom Shop” logo at that point.
Masterbuilts are pretty exquisite, for the foreseeable future you are only going to get them used, as a NAMM guitar, or as special runs from the big Jackson dealers who have the influence (and build slots) with Jackson to make it happen.
Production Select vs MIJ, my experience is that the difference is in wood quality and the USA instruments have a slightly better fit/finish/attention to detail (e.g. the cavities and routes on my USAs look like furniture quality woodworking… especially my Custom Selects, the MIJs are no slouch either but the details are a notch higher on the USAs). Only you can decide if that is important to you.
Now this is what I will tell you: I put in an order for a Custom Select Soloist in August 2020. The delivery estimate was 18-24 months. In August 2021my dealer checked the order status and was told we were still “still at least 24 months out”. I said “fuck that shit” and cancelled the order and got a full refund.
So at this point you realistically have four options (unless you want to wait 24+ months to get your guitar: a used Masterbuilt, a dealer spec’d or used Custom Select, a USA Select (used or new), or MIJ (used or new).
In my experience a used Custom Select can offer a good value. People will mark them up and try to sell based on the custom shop badge, but they are harder to sell. They are one offs or part of a spot run. It is harder to sell unique and hard to verify instruments. So with some wily negotiating I have seen people get used Custom Selects cheaper than used Selects… but you have to work the deal.
Sellers try to blur the line on guitars with a “Custom Shop” badge. There is a big difference between a Master Built and a Custom Select. Some sellers are more than happy to let you believe a Custom Select “custom shop” is a true Masterbuilt Custom Shop. Badged guitars should have a COA and that is the easiest way to tell what a “custom shop” Jackson is. It will state “Masterbuilt” or “Custom Select” on the COA.
At this point, I am down to 3 Masterbuilts, 2 Custom Selects, 1 USA Select, and 2 MIJs.