You were using very weak concetration of HCl, if I'm not wrong, 3.33 %. That cannot eat metal fast. (good)
I think that you cannot have little chunks of metal because of acid, couse acid would eat metal 'in layers' (dissolve kinda) not making chunks, except if you have metal posts that can be removed from somewhere (not likely), but the only thing that comes to my mind are the turbulators inside heater core tubes, they are small enough... (also not likely)
When I was flushing/testing my system I also got small black chunks coming out from the system, and I found that that were little pieces of black sealing silicone (I used that for sealing the parts of the heater core.
IMO, you should be careful putting acid into the system, you don't want damaged heater core/rad tubes, they are really thin, also, the pump rotor axis, holding the impeller is also metas (in my pump). If you put it, just make sure it won't stay too long in the system...
As for clogged blocks, somebody with more experience is needed here...
To be honest, I have no more ideas what are and where from are coming those black chunks...
