Suddenly it is harder to pedal This is related to a previous post, but I thought it best to just start with a new post.

My local bike shop installed an 8 speed indexed shifter on a Huffy MTB which has a 6 gear freewheel. 

About 2 weeks later, it started being harder to pedal when in several of the lower gears.

I had to stop several times to move the derailleur and chain a little to get home.

Could that possibly be caused by having an 8-speed shifter with a 6 speed freewheel?

(My bike shop is awaiting a Shimano Tourney Tx50 3x6-speed Thumb Shifter Set to replace the 8-speed shifter.)
If you noticed the chain chattering on the sprocket, then yes, it could be caused by using an 8-speed shifter with a 6-speed freewheel. With indexed shifting, all the drivetrain parts are designed to work together, and if you've got a mismatch--as you do here--you can expect the shifter to pull the chain out of alignment with the sprocket.