I had a spare set of wheels from my 09 GT GTR S4 road bike and I was going to put them on my spare denali road bike. However there is a small gap in the rear wheel, between the wheel hub and the frame. What options do I have? Currently the wheels will work and the gap disappears when I tighten the hubs... But the skewer seems rather short.

A road bike is a road bike, ie it should have a 130mm gap between the rear dropouts.

If all is as it should be, no problem.

But if you have to squeeze your stays together to fit the rear wheel, you can use that space to make it stronger. Add a spacer under the left locknut to fill the gap, tighten all the NDS spokes 1/2 a turn or whatever it takes until the rim sits in the same spot when you flip the wheel, bingo.

Thanks for the input. I've gone ahead and measure the wheel width at 130mm but the frame drop outs are about 135mm? So I'll definitely try your suggestion, but how do I order a longer squewer that is not as short as the current one, but not overly long?

135 mm is MTB size in length (diameter is the same). So if you order out of the MTB section of the catalog you should be good.
The only overly long skewers I've seen came with a tackx trainer. But even that is a non issue. Any excess will simply protrude beyond the nut on the other side and can be trimmed off with a hacksaw.