The spray-on poly works really well. It's more expensive to buy it in
spray-cans than by the quart, but you can do nice thin coats without
brush marks or drips. Just sand with a really fine grit in between
coats.

If you haven't done your final coats of Polyshades yet, consider buying
yourself a cheap air brush (I got one for $29 at HD or Lowes) or HVLP
gun (Harbor Freight has one for $45 or so) that you can hook to your
compressor, if you have one. A big chunk of that cost could be made up
by the fact that you wouldn't have to buy the clear finish in spray-can
form. The air-brush technique works really well with the polyshades
because you are applying it very thinly, and you have a lot of control
over how dark it goes on. When starting from scratch you can just
apply it in thin even coats until you reach the desired color depth.
In your case, you already have some areas that are darker than others.
With the air brush, it's a lot easier to selectively coat the lighter
areas, avoid the dark ones, and generally even up the color over all.
There's a lot of overspray, though (not so much with the HVLP gun) so
definitely make sure you have good ventilation and where a respirator.
And don't do it in your garage right next to your vintage mustang ;-).

There's no need to do additional layers of clear finish unless you
effectively have fewer than three coats of the Polyshades (keep in mind
that you wiped most of it off on your initial coats).

By the way, it's not so important with oak, but for woods which tend to
absorb stain very unevenly (pine, maple, etc.), results tend to be
better when using a sprayed-on die or toner like Polyshades than with
traditional wiped-on stain. The only real disadvantage is that a nick
or scratch which removes the finish will show bare light wood
underneath; with wipe-on stain the color penetrates fairly deep into
the wood.