Always happy to help out!
In response to setting up the stack, if your soundcard has an optical-out, you can use that to connect your Modi 3; you'll just have to set the soundcard to output the digital signal that way. Otherwise, use either USB or optical from your motherboard (some motherboards sound better one way or the other; mine in particular has a really bad SPDIF out, and marginally better USB).
From the DAC's SE outputs, it's a simple RCA cable to the amp. That part should be pretty easy.