yes, youve altered the intake and the exhaust, which ultimately alters the air/fuel ratio.
if you want it to run like it did, put it back the way it was.
if you want it to run correctly with your chosen mods, you'll have to make jetting changes.
Runs on a dyno are your best bet to getting it right.
This is a forum for SOHC Hondas, if you have a 79F, its most likely DOHC, and this thread should move to the Other Bikes section of the forum.