If you go to what you list as chain 1 and swap just the cartridge (Put the AT in place of the EMT), the system should play fine. Even if you don't plan on using your setup this way, it will be a good check to make sure that nothing in the system is damaged.
Going back go chain 1 as you list it. There is one simple thing you can try. I would give it a 50/50 chance of working. Remove the xlr IC's going into your Pass, install the jumpers between pins 1 and 3, and use a pair of single ended rca IC's instead. Going single ended will lower the gain of your source, and may be enough so that you can use your EMT. This is something that you really should try. I think it has a good chance of working.
Going back go chain 1 as you list it. There is one simple thing you can try. I would give it a 50/50 chance of working. Remove the xlr IC's going into your Pass, install the jumpers between pins 1 and 3, and use a pair of single ended rca IC's instead. Going single ended will lower the gain of your source, and may be enough so that you can use your EMT. This is something that you really should try. I think it has a good chance of working.