Start here > http://motorbicycling.com/showthread.php?t=22726
Your clutch cable is probably not tight enough. Too bad you diaassembled the clutch. Now you'll have to start from scratch to readjust it. Follow the steps in that thread and it will probably answer your questions.
The bike will never pedal as easy at it did without the engine. There will always be some parasitic drag from the chain/sprockets and the clutch cross shaft and other rotating parts. If the clutch is adjusted correctly it can be pedaled, but it won't be as easy as you might want it to be.