I inputted the notroll address I used port 6332... but when the miner started it switched over to the stratum pool of port 3333. Is this normal?
Yes, stratum mining switches to a different port. It's more efficient too.
And how do I get my coins back into my litecoin.org wallet?
Open your Litecoin client. Click on the "Receive coins" tab.
You can see your Litecoin address there. Copy and paste this address into your "Withdraw" address in the mining pool website.
Then, set your mining pool account for auto-withdraws or click on the button to withdraw.