I do believe there are direct connections from places in SE Sweden to Tallinn as well. I don't know if you have to go all the way to Stockholm to catch them.
Typically when I am trying to get down to Europe, I take a ferry to Stockholm and then run straight down to Copenhagen via Helsingborg. The ride takes about 7 hours or so if you don't stop for much. Realistically you could be in N. Germany via Femahrn in a really long day's ride of about 10-12 hours. Depends on your endurance, but when you compare what Finnlines charges to get you from Germany to Helsinki, you'll find you will save a lot of money. Just a thought for you.
A couple of points about the riding part from my experience. This summer on my way back from Italy I did Warsaw-Tallinn in a single 14 hour stretch. It's about 950km as I recall. Via Baltica is generally acceptable condition. However, from the Poland-Lithuania border SW to Warsaw, or W to Gdansk, the roads are pretty rough and tumble. Not much out there either aside from the city of Alexandrow. I would be sure, if I were you, to have your things in order before getting much south of Kaunas in Lithuania. Just a word to the wise. I wasn't aware that corner of Poland was so empty.
BUT...if you are riding a BMW bike, there is a dealer in Alexandrow for your information.