The main problem comes from the large 2.11" intake valve. It will interfere with the small bore on the 326 block with a high-lift cam, and breathing will be inhibited due to the shrouding of the valve by the small bore.
I like the 326 engine, but if I was going to spend the $$ on a stroker kit I would definitely spend a couple hundred more and start with a 400 block. The 400 block is still pretty common and not very expensive. Then you can use the 'good' heads and make the most of them.
With the 400 block you can use the 326 crank (same as the 350 and 400, 3.75" stroke) and end up with a 406 or 412 depending on bore size. You won't need a stroker kit and you get a bigger engine. More power with less money spent than with the 372 from a 326 block.
Or stroke the 400 and end up with a 461 or 467.