The heads shouldn't be an issue, unless they're shot. Were they rebuilt?
Earlier you said lifters, which is it? I would check part numbers on the lifters (if that's what we're really talking about) and see if they cross reference to both engines (3.1 & small block).
Since the parts store only sells the one length pushrods, for you to get different length ones would be a packaging mix up from the manufacturer.
To me, it sounds like you may have some valves that aren't closing all the way, or maybe not opening. Are you getting any popping out of the exhaust or intake?

 

right yea the lifters i got was from a small black 305/350 is that they where for. and from what i'm seeing they don't seem to be crossed with the 3.1 according to summit. do you think they could be to short?