I find the liturgical and rabbinic descriptions of the atonement process on Yom Kippur challenging. Without a Sanhedrin to mete out punishments for intentional sins, and no altar to bring offerings to atone for unintentional or un-witnessed sins, the chance of ever starting the year with a clean slate seems bleak. But we aare also led to believe that sincere repentence wipes out all sins. Can we ever start with a truly clean slate? Or will we still be held liable for sins we don't get punished for in this world?
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In summary, no, not ALL sins.
There are several aspects to answering your question, and I couldn't get to all of them, here.
But to start, Talmud Yevamot (don't know exact page) explains that Yom Kippur never atones for sins between one person and another until that person requests forgiveness, personally. The method becomes a bit more complex if the wronged person is unreachable or dead.
Another more difficult example is atonement for lashon hara and rechilut (gossip, slander). How would you now how many people got the bard word about someone, and how could you really recover the damage already done?
Yet another concept is inferred from your mentioning that we don't have a Bet Hamikdash and we carry the sins of our ancestors. This concept is hinted to in a few places in our daily prayers (esp. Tachanun) and the fact that we still don't have a Bet Hamikdash is an indication that we have not yet been forgiven.
Finally, what about all those sins that we did during the year, but on Yom Kippur, we forgot about them and didn't mention them in our confession? We're still responsible.