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Gozaimashita is the past-tense form of gozaimasu, which is the polite form (the -masu form) of gozaru, which is a polite word for aru (there is).
So, afaik, arigatou gozaimashita is often used to thank someone for something that has already happened, some sort of finished action, for example if you thank someone after ji-geiko. Arigatou gozaimasu is used to thank sb for sth that still lasts or has a certain effect on the present.
But often it's very difficult to decide which form might be appropriate, so the lines above are only a short explanation. I hope it's not too difficult to understand because it isn't that easy for me to explain it in english
In some cases, the vowel is spoken, just not quite as forcefully as the other vowels in the word. For example, sukiyaki is pronounced "skee-ya-kee", but from what I've been told, there is a slight prononuciation of the "u", it's just not heard by non-Japanese listeners. That may or may be correct.
In many languages, you will find a process called "elision". In English, dropping the "g" on participles and gerunds is a form of elision, although not a correct use. If, for example, "la amore", a phrase in Italian, is spoken, it actually is pronounced "la-mo-ray", spelled "l'amore", etc. That's why you'll see apostrophes on some European words and names.
I have seen a lot of people try to learn japanese on their own and mess up because its so different from english its hard to remeber. Have somone else thats interested its better to study with other people.