Ok so when ever i type the keys ( or ) they are on a different key like ( only works if i type 8 in japanese and ) only works if i type 9 in japanese, also 「 only works if i type ] in japanese and 」 only works if i type \ in japanese, additionally, if i type 。 and i cycle through the options i cant create the eyes for kaomoji and lastly i cannot create the ~ symbol in japanese, among other problems, i have no idea what i did wrong but I would really love to fix it!
( only works if i type 8 in japanese and ) only works if i type 9 in japanese
Not sure in how far this is related, but I'm on a German keyboard here and 8 and 9 are exactly the keys designated for the parentheses on it (I actually use the US layout though, so I need to press 9/0). A physical Japanese keyboard would look similar, I guess?
Anyway, you didn't tell us which IME you're using, but if it is anything like SCIM+Anthy, you can just re-assign the keys as you see fit, as well as add new dictionary entries and manage those using something like Kasumi.
Refer to your IME's manual.