I am looking for a classical nylon stringed guitar for under 400$. I went to a musicians friend clearance center the other day and saw a lot of great guitars but wasn't sure what to look for in a classical. Also, if the guitar either is acoustic electric or has the capability of doing so later on down the road, that is preferred, but by no means a requirement.

I'd take a look at some La Patrie's. I got one when I started out on classical and it was worth every penny. I still have it alongside my newer one but that thing sounds great for the price. Really nice feel too. Just find the one that fits your price range and give it a test run.
See if you can find any Alhambras for that price. Admiras, Cordobas, Almansas around that price have been recommended on here. Make sure you try and try and try again before you buy. You might find something interesting for a nice price that you haven't heard of before.

As for the electronics, well, I'm not really an expert on this but from what I've heard the decent ones go into a higher price range.

You'll have to weigh the options out before you buy. Maybe spending more now is better, or maybe it's better that you should not spend much and save up for a nice guitar if you start gigging or anything like that.

Good luck.