ya << to <> shi "and"
"ya" lists an incomplete group of things (implies there are other things too which are not explicitly stated)
"to" lists a complete group (all elements explicitly stated)
"shi" is used after phrases (not individual nouns), indicating an incomplete listing of reasons for something.
demo <> keredomo <> ga "but"
"demo" - this is actually the "TE" form of da/desu plus the particle mo, so it's actually more like "even so" or "however"
"keredomo" - this is a pretty polite way of saying "but"
"ga" - is a conjunction meaning "but"
dô <> ikaga "how"
ikaga is more polite.
koto <> mono
these are difficult because each word has various uses, some of which overlap.
koko ni <> koko de "here"
"koko" is irrelevant here. The hard thing about particles is that what they mean varies slightly from verb to verb, it's not just a question of what comes before the particle.
kata <> hito "human being"
kata is more polite
naze <> dôshite "why"
basically the same, but "doushite" can also mean "how" in spoken Japanese.
doko e <> dochira "where to"
dochira is more polite
totemo <> domo "very"
probably shouldn't think of these as a pair, even though they are very similar in meaning. There's so many other words that also mean "very":
Alternatives to saying totemo | nihonshock
"doumo" is literally something like "no matter how/what", doesn't fit everywhere that we would use "very" in english. It also is used to mean "thank you".
dozo <> onegai shimasu "please"
"douzo" invites someone to do something (which benefits that person)
"onegai shimasu" is the speaker requesting something which benefits the speaker.
ii <> yoi "good"
"yoi" is the form that is used when conjugating "ii", you can use it instead of ii (un-conjugated), but it sounds a little old-fashioned. common in anime/manga.
hanashi <> hanasu <> hanasu koto "speak" (besides: when are forms like hanashi used?)
too big of a topic to answer here, sorry...
da <> de (wa) <> na "to be"
not sure exactly what you're asking here. da is the "to be" verb, "na" is the form of "de aru" that precedes a noun, but you mostly only see it in na-Adjectives. "kirei da" + "hana" = "kirei na hana"
de is sometimes (not always) the TE-form of "da/desu/de aru"
Hope this helps!