'66-'68 BB's all used the same 827 and 828 exhaust manifolds; don't know about the sidepipe differences (just the pipes, not the covers) from midyear to C3 (they were only available on C3's in 1969).
There is apparently a difference - the P&A30 Corvette parts book shows '65-'67 BB sidepipes with the same LH/RH part numbers, but the '69 BB sidepipes have different part numbers (don't know what the difference is).