Try resetting battery, are all wires hooked up correctly? Make sure hose that you disconnected to put seafoam in is reconnected, also when I seafoamed mine the spark plugs became found so I changed them out.
I seafoamed today and I also had rough running for about 20 minutes than nice and smooth. I ran a whole can through brake booster line and than I put half in oil and half in tank, I than changed my oil.