On Youtube I stumbled upon a documentary about core drilling in the Antarctic and it got me thinking.
When/if Pangaea existed would it have effected the Earths spin/axis/orbit? ...
(I assume you meant 'affected'. Pangaea didn't effect (causally create) earth's spin because the earth was already rotating long before the pre-Pangaea supercontinents formed.)
If you're referring to radical effects such as huge / catastrophic planetary wobbling or flip-flops, the answer is 'No'.
At the scale of the entire planet the effects would have been relatively small - the sort of changes it would take today's precise sensing technologies to detect.
In proportional terms the earth's solid crust is a very thin skin floating atop a largely viscous mantle / core complex. In addition, the crust components are less dense than the vast majority of the earth's bulk that underlies them. In other words - the outer crust represents only a very small fraction of the planet's mass, it has no solid connectivity by which to leverage the mantle beneath it, and it can't jerk the whole planet around.
The surface weight distribution isn't all that non-symmetrical once you recall that the oceans themselves weigh a lot.
Wegener's original theory was framed with regard to the continents as we traditionally address them - the masses extending above sea level. If those widely scattered chunks were the only bits moving around, it might suggest some effects on planetary orientation, wobble, etc., as they skidded around the surface. Wegener himself seemed to think the planet's rotation provided the motive force for sliding these visible continents around. One reason his theory lay unaccepted until after his death was that calculations indicated rotational (etc.) forces weren't strong enough to explain continental movements.
It wasn't until we discovered (a) a worldwide set of tectonic plates (of which the traditional continents are merely the tallest areas) and (b) the mainly mid-ocean ridges and subduction zones that we recognized it was these larger units that were in motion and the missing motive force was convection from below.