Sorry for the slow reply...I didn't realise you had posted the recipe, sorry.
Your idea looks like it will work or at least get very close. Give it a try.
I can't seem to imagine karo and melted chocolate working the same because I think it would not be as thick as molasses, or am I wrong there. Try your idea first. If it doesn't work try using glucose syrup. Glucose would give the same thickness as molasses with out imparting any flavour.
Apart from what to use as a replacement for the molasses, I see no reason why you can't just change all the dry spices for cocoa powder.
Another thought I have just had...You could try a caramel sauce made from sweetened condensed milk. You use canned milk, it must be sweetened condensed or it wont thicken and turn caramel. Remove the labels and put the un-opened cans in a steamer or a pot of boiling water. Steam or boil the cans for at least 90 minutes...longer the better!! 2 to 3 hours would be good. Let the cans cool and presto...thick caramel sauce!
Oh...yeah...Don't let the water boil dry!! If even one can explodes you will know all about it !
The only other thing I see which might be a techy prob is your idea of 1/4C cocoa. I am assuming that the "t" is teaspoon. So I would agree that you need to up the cocoa for flavour. As I say try it, but if it turns out too dry, try dropping the flour to 2 1/4C or maybe even 2C...But looking at it, the flour should be OK at 2 1/3C. If adjusting the flour does not work, then try 2 eggs which will compensate for the extra dry in the cocoa powder.
That is it...as long as you use a nice thick sticky gooey syrup, your idea should work.
Lets us know how you go?