I don't think getting a brand new custom shop Jackson is cost effective unless you are using the "$250 other body shape" option. Your RR1 looks pretty stock, so I'd save the money.
As for the custom RG, there are a lot of RGs already. Determine what you really want out of your custom, and see if Ibanez currently makes it, or did recently. If so, get one of those. A high end RG is a mighty guitar, so that would be my first choice.
If you can't find you want, then I'd suggest a total custom, and not a copy. Your two choices aren't exactly similar (other than being electric), so think about what it is you really want and get someone to build that for you. Keep in mind though, that custom guitars, including Jacksons, can have you waiting 9 months or more for arrival. Look at LGM's Leviathans, they are very similar to Jems in regards to neck feel (or so I'm told), but with more options and a unique shape. Check other builders too, if you want. But first, decide what you really want, not which of two is best. then, you're half way home.