I'm not worried about gear, but the the route and the permits I would need.

You can apply for a permit 168 days in advance. It's actually a very simple application, but make sure to apply exactly 168 days before your start date, because it is a very popular route. If you don't get the permit, you can still apply as a walk-in. The route is well traveled and easy to follow.

Should I go north bound or south bound?

Either way is fun. It's all personal preference. You end your hike with a summit of Whitney if you go southbound, though, so that is the more popular direction.

What paths should I use? Where do I start hiking? Is it safe to go alone or should I bring my dad?

You sound like you could use a trail guide book. Here is a good list of resources.

The JMT is a well beaten path and I dare say you will rarely be alone on it, especially if you go during the high summer months. Maybe take a wilderness first aid course if you are concerned about a solo hike.