They wont run poorly. Just wont make tons of steam. If you can't sell them or can't afford to buy new then i would use them for the time being. It just means a future rebuild and more money later if you decide you aren't satisfied with the performance.
If it were my money and motor, and was forced to use those heads, i'd take the money that would have been spent on the stroker and have the heads and intake ported and put on a 302/306. Its a hard decision though, as that isn't "ideal" either.
Try and score a deal like addermk2 did if at all possible. Shop around for better heads, but if you have to use them then you have to use them.
About the AFR vs Trick Flow. old and beat'n topic so i'm going to avoid an argument. They are all good heads that can and have made good power. I've even made recommendations for 4 different manufacturers, so i'm not biased. AFR's don't always out power Trick flow, and vise versa. The combination of parts around the heads counts a lot.
I'll just mention this, look up NHRA class rules. Most classes have a weight penalty if you use Trick Flow heads that the AFR heads don't have. You don't get weight penalties because the you are inferior.
