I think the most difficult part if Japanese for me has changed as I learnt more japanese right now i'm at the imtermediate/advanced level. Meaning grammer is advanced but my vocabulary and kanji knowledge is intermediate.
1)Right now i'm finding learning all the words is just daunting. I read an essay in my kanji book about how trash is becoming a real issue in tokyo and what people can do to help aliviate the issue. There's were about 50 new words in that one essay.
2)I also find that since I learnt correct grammer first it's sometimes hard to understand my friends when they speak or write to me. I have a friend who messages me like i'm Japanese. She knows i'm not japanese and i've never lived there but since I understand 99% of what she says so she has become comfortable speaking freely with me. But the truth is sometimes I have to sit and read what she wrote like 10 times cause I understand all the words and particles but can't figure out how to make sense of it all. Cause she' using normal Japanaese grammer when I learned ultra correct japanese grammer.
So I guess my biggest problem is what you said. The textbooks don't prepare me for normal japanese.
oh if you're a beginner I know this excellent book. It was my first japanese language book and I think it laid a wonderful foundation for me. It's all conversation. It has no translations in it. It only translates new words that turn up in the dialogues so it's up to you to figure out how it all works in a sentence. It was hard at first but the pay off is well worth the headache.
Amazon.com: Berlitz Basic Japanese (Berlitz Basic Language Course): Books: Basic Books,Berlitz Publishing Company