What you described is what others call a dry hit. It's a harsh, scratchy, almost burning sensation at the back of your throat. You still get vapor, you still get flavor, but it's irritating to say the least.
So yeah, you should be good now that you've given the new head time to soak in the juice. If you vape too fast for the coil to wick then you're going to start getting dry hits again, which is possible in a mini PT2 with a 50/50 juice, so if it starts happening again just slow it down, or do a couple of unpowered hits to get some juice to the coil before you hit the button.
If you get that feeling after letting it sit for a good while then you may need to try toning down the nicotine level, which is the predominant factor when determining throat hit. There are of course other things that contribute, but nicotine is the #1 throat hit source.