1. I am not really sure. If I find out a definite answer, I'll edit it into this post. I would assume that the only thing that would still stay in Japanese characters would be if you named yourself/your rival/your Pokémon in Japanese characters. Even in the Japanese version, you have the choice of using English or Japanese characters when naming yourself, your rival, and your Pokémon. Once again, I am not sure, but I think that the natures and attacks would change to English if your Pokémon were traded to an English Ruby/Sapphire game.
2. It shouldn't be too difficult, there are several people playing the Japanese version that don't know Japanese. The gameplay is mostly the same as the old R/B/Y games, except for a few changes, like the islands that you can get to after getting to Cinnabar Island, and after defeating the Elite 4. And now, to get past the guards that block your path to Saffron City, you will need to give them Tea that you get from a lady in Celadon City, instead of Fresh Water, like in R/B/Y, and the new move tutors, etc. If you pretty much know how R/B/Y worked, then you should be fine.
3. Your PM box can hold a combined 70 sent/received PMs. Have you tried switching your settings on your Private Message screen so that it will display older messages? Try changing the settings on your Private messaging inbox screen so that it says "Show messages from: the beginning." That could bring up some old PMs that you don't know you have, but are still counting towards your total of 70.
4. If you trade a Pokémon from Fire Red/Leaf Green to Ruby/Sapphire, then you should get the National Pokédex on Ruby/Sapphire.