I agree that if the engine is out, there is good logic to adding the stroker kit now. It's relatively easy to add ported heads and a solid roller cam later. It's good logic, but it's not the best bang for the buck logic.
If you compare, as you said, 1) adding 29 cubic inches with a stroker kit to: 2) Fully porting the heads and putting a solid roller cam. There is no comparison in terms of power increase.
I would add that adding a roller cam could cost much more than that if the rest of the valve train needs to be upgraded. That's for sure a possibility.
On the other hand remember that we're talking about out of the box Edelbrock heads. They don't flow a lot. Slightly better than factory 428CJ heads. There's huge gains to be made there, in my opinion. And they'll become even more of a restriction as the displacement goes up. That can be offset to some degree by using a bigger cam, but not completely.
In my opinion, If I had say $2000 total to spend, and I wanted to increase power, I'd get the heads fully ported and milled for more compression, add an aggressively lobed, higher lift, and bigger duration solid flat tappet cam, and then work on the intake/carb combo. Maybe port the intake and add a tapered or open spacer. Add a used bigger carb if the current one is too small. That'd get you way more power for the dollar than simply adding 29 cubes. It's no contest, in my opinion. I don't see how it's even defensible.
Keep in mind that we're talking about a medium weight car with a 5 speed tranny, and I'm guessing on street tires. Do you want more low rpm power? I wouldn't if I wanted to go fast.
JMO,
paulie
edit: typo