Troubled 2.5

Hey all, I've got a 91 Sonoma with the 2.5 151 in it and she's struggling. It's misses something fierce at idle, low, and high speeds now. It's also got a bad knock that I thought was valve train but after new pushrods and lifters last year, figured out it's rod knock. So I'm gonna pull the ol thing out and go through the whole thing here soon. At this point I'm asking purely out of curiosity because I'm doing a full overhaul. But I'd like to know what may be causing the issues. I've pulled the clogged cat off and got a new muffler on there. Pushrods and lifters (as I said), new coil, plug wires, and plugs gapped to 45 thou. I haven't touched the fuel pump or egr stuff on it and I'm thinking the egr may be the culprit. Just looking for anyone else's 2 cents.
Thanks for reading 👌