That's exactly how a person can ruin an entire project in an instant. Just doing things does not work for me in woodworking. It almost always results in a complete disaster. Approaching anything in this manner requires knowledge and experience, two things I do not have in finishing.
Thanks for all the tips. Due to time constraints during the install, and not wanting to stop and figure out a better way as i was in the middle of installing, i just applied some stain to the ends, and actually its come out pretty good. Not bothering me at least, and that's good. As its the little things that bug you sometimes.
I'm not a home builder or renovator, but I would consider removing & replacing the old stair tread and riser facings entirely. If that isn't practical, I would probably go with a circular saw + straightedge, followed by an inexpensive flush trim saw at the ends, and a sharp chisel for final cleanup.