Sorry, OP, but you should ask the questions and do the research before you do the work. *

Didn't know that would turn out to be an issue or I would of asked up
front :O/

As FF noted, pine is a funky wood to stain as it gets blotchy without pre-treatment with a wood conditioner/sealer. Stain is not a finish treatment, so you should have planned on topcoating it anyway. *Since your major objection is the difference in sheen, any polyurethane, varnish, really any clear coat at all, will solve that problem.

I identified the worst shiny places and sanded them with a small
electric sander and some rough paper. I blended and feathered the
sanding and then went and re-stained the sanded spaces and feathered
that back out along the boards. After drying the shiny spots aren't
so shiny (at least no harsh edges to the shiny areas). Might leave it
but if it would be better protected with something and that something
would also give a little more uniformity then all the better. Also
some of the knots had fallen completely out so I filled the holes with
stainable wood filler and then stained them with a small artist brush
the same color as the rest of the knot. Worked out pretty good (a lot
better then BIG holes in the wood). The knots and odd grains in the
wood pretty much assures us this won't look fake regardless of what we
do.

Thanks!