Don't worry about lining up the transom with the end of the strakes.  Just set it slightly inside the strakes and wrap them where the strakes feel like they line up the best.  Any small overhang off the back can be trimmed off with a pull-saw after the epoxy has cured.  The angle doesn't have to be perfect as long as it looks pleasing to the eye.  A helper is almost mandatory as you will be twisting the wood.

Use a metal tape (or one that won't stretch) to measure from the bow to each upper corner of the transom.  Adjust the transom until the measurements are the same.  Pull the same tension on the tape measure as you measure each side.  Look at the down-ward dip in the middle of the measuring tape.  The dip should be about the same (same tension) when measuring each side.  If the strakes still extend more on one side of the transom than the other when the transom is perpendicular to the centerline, then the side with the longer overhang does not curve out from the center as much as the shorter side.  If the overhang is a lot or you are a perfectionist, you can loosen the stitches and adjust until you're happy.  Good luck.

Thanks for the advice.  I'm amazed by the immediacy of the responses and grateful.  I'm building in Australia, but feel as though there's a huge group of fellow builders round the corner eager to help and forthcoming with assistance.  Cheers.  Incidentally, somehow I've positioned my bow seat support 1" closer to the bow than stated (probably a mental mistake in converting from inches to mm).  Surely this is inconsequential?

"... inconsequential?"  Most likely.  If John Harris inspects your Wherry, he'll notice.  But he won't kick you in the shins.  However, you should think of a good technical reason for why you modified your hull.  Something like you wanted a bit more room to stow your emergency paddle flat on the bottom strakes. :)   Good luck with the rest of your build.