I don't know about out-of-region eShop access, but consolidating your games should be doable if the US 3DS and the Japanese New 3DS are on firmwares below 11.4*. If you follow the CFW guide on
http://www.3ds.guide/ for both the US old 3DS and and JP New 3DS, you can use GodMode9 to create .cia versions of your US games, then install those cia files on the New 3DS using FBI. The purchases will still be associated with the US old 3DS/US NNID, but they'll also be installed and playable on the New 3DS. The games on the JP old 3DS can be installed the same way if you hack it, or you can transfer them using the built in official method.
*After CFW is installed on a system, you can safely update it to 11.4 without losing the CFW. You just can't install CFW directly to 11.4.