^Hi winner! welcome to the party!

1) Magic stones are also worth using later on when you're running special dungeons (either as a continue option, or stamina refresh for limited time dungeons). at early ranks it's not really worth it since low level special dungeons have shitty drop rates and your magic stones are worth more than that. Not sure about the next jp godfest since I'm not sure when the next event is. Nothing's announced for the moment! Oh, and you will need to expand your monster box with magic stones too, so always good to keep a couple on hand even after rare gachas.
2) You can use your magic stones on the batman gacha! Special monsters and it's a limited time event so...yeah.

You might even get something good! I haven't pulled it yet but I might before it ends.

I'm stingy with my stones.
3) I usually wait for events where they put special monsters into the PAL machine. There's no event going on now so I usually save my Pal pulls until then. Plus, if you accumulate your pulls and roll them all at once, the chances of getting something better is oddly higher.

3) Currently the special dungeons that are running are Wind Mechdragon (you might not be strong enough to clear it yet, and even if you were, the team cost of the mechdragon is too high for you to use right now), Batman collab (drop rates are low at the lower levels, but you can try if you want), Pierdra (I recommend this since the Pierdra is a useful toy dragon with double element resist). You might want to wait for the 1.5x drop rate for the Pierdra dungeon though, every little bit of extra chance helps ^^ There's also the weekend dungeon that you might want to run a couple of times to build up coins, but your main focus should be the normal dungeons for now. The more dungeons you clear = more magic stones, and better grade monsters that drop. You can either keep those mons or feed them to your team to make them stronger ^^ Plus the sooner you unlock technical dungeons, you can start farming for pengdras to evolve with the colored dragons and evolve your monsters even more quickly.
5) Pad wikia has tabs on the home page for the NA schedule and JP schedule. I also follow a few twitter bots for reminders on the daily special dungeons, and I go to
http://www.dopr.net/pad for extra info.
www.puzzledragonx.com has decent information on the dungeons (monster strength info primarily, you can gauge if your team is strong enough to beat a dungeon) and a more accessible layout for their monster book, but Pad wikia is good too.
There's a lot more, but yeah, this is a start. It's good to look up the evolutionary paths of the monsters you have and are getting, and deciding whether they're worth keeping for the long run or are just good for fodder. Some monsters are good enough in early/midgame, but your late-game team usually evolves past that. Plus there are many types of team strategy (the glass cannon strategy that piles on the attack multipliers, the turtle strategy that absorbs hits and whittles away at the enemy, or the zombie strategy) that require different play styles and team setups. There are mono color teams, dual color teams, rainbow teams, or teams that are grouped by type (my team is dragon heavy for example). A lot of it is luck of the draw, so depending on the kind of monsters you get, you shape your strategy via that. You'll have an easier time on some dungeons and a harder time on others depending on your team balance. I'm no expert, but I'm learning too

reading about strategies on the wikis help!

/endgeekrant
Hope it helps!