Ive not heard of someone plugging a reader in and causing a problem. That just does not sound likely.
And as said above, the 410 code won't stop the car from running well.

I'd shut it down and disconnetc the battery for 1/2 minute or so. Reconnect and see what you have. Could be the ECU is off in space and could use a reset.
Other than that, it's time to look at basics: You know you ahve spark cause it's running. I wonder what the fuel pressure is - very low pressure will give you the symptoms you have, another cause can be a messed up throttle body.