So, I have figured out what was going on, and my have a fix.
1. This is fixed. Setting it to horizontal-lr was the fix. I was still looking at the old file when I thought this wasn't working.
2. I understand now that the text wasn't "showing through" but was actually being written after the magnification text block.
As a fix, I'm placing the entire text in one div container. Then placing the two separate text files in div containers with display:none. I'll call those containers with the magnification app, and hopefully that will do it. Uploading the test now.