To me, the biggest limitation of the J-series is lack of logical-router support. However, since you have so many real routers, that may not be as big of a deal for you.
I believe that the J-series will do most of the things you mention, but some features will require additional licenses. For instance, regular vanilla BGP is standard, but I believe VPN PE configurations will require and advanced features license. I'm not an expert in licensing, but if you don't have the required licenses you may need to go back to your source for the routers and/or JUNOS to aquire them.
And of course you won't be able to practice interface-specific commands, such as NBMA on ATM. Personally, I think practicing the ATM and FR parts is overrated anyway as long as you can remember the ramifications of such topologies. Since you got it right (or close enough) in the JNCIP, you likely won't have much problems memorizing it for the JNCIE... or at least memorize where to find it in the reference material.
If your concern is the number of interfaces to interconnect the boxes, use a hub and VLANs. This may be a good idea anyway if you have your boxes separate from the room where you actually study (which is especially likely if you are in a hot weather area like I am). This way you connect all of your boxes physically to the hub, then provision VLANs as you need them without having to re-cable.
Another thought is that if you are following the study guide, most of the examples of the advanced topics only use a few routers at a time. That is, the first large part of the JNCIE is similar to the JNCIP with a huge network to troubleshoot, but the MCast, VPN, COS parts of the book generally only use about 3 or 4 routers at a time.
-Jeff
#J-Series#study#JNCIE