While there are some critical differences (bore/stroke for example), I'm willing to bet the majority of it is related to different dynos.
The 76x94 engine combo would likely produce more hp where your 82x90.5 would produce more torque. No telling about those heads, but I run Denham heads and know how well they flow.
You didn't mention your rod length in your 82 stroker, but check the rod ratio differences to account for some hp/torque differences.
Then there's the simple state of tune of each engine. Timing, jetting, air/humidity, fuel, etc...