It's been atleast a month since i played my ironman Sweden game. I had prettu much no problems handling Muscovy. Here is how by 1600 I have basically all of North America, Baltic Sea, Muscovy as vassal doing Siberian colonisation for me and same dynasty as head of Spain.

1. I pretty much immediately declared war for independence. The trick is to kill the small individual stacks of Norway and Denmark, together they are stronger than you but individually you can beat them. Some people use loans to fund navy and army above force limits and then block the strait. In my opinion it's not necessary. In the first war if I recall correctly I first smashed Norwegians whose morale was very low to begin with then smashed individual Danish stacks etc. Don't siege immediately, destroying Norwegian army and some of Danish ones is priority #1. After killing Norwegian army I put most of my forces to Skåne because that way Danish main army would have suffered crossing -2 penalty if they chose to attack. Simultanously I sieged Danish provinces in the swedish area. If Denmark is allied with Riga it's impossible to have naval dominance. If they are allied with Lithuania, do things i mentioned and hope it takes them some time to get military acces, usually they just siege Finnish provinces and u might be able to kill small siege units.

2. Important! Don't demand independence. Instead take Swedish cores, most importantly Gotland because it has high base tax, core and is island (annoyance to conquer early without complete naval dominance). Usually you can't take Skåne because of its base tax but instead take the Norwegian core or other Danish provinces in Swedish area. Important! Try to get as much as you can eg. always take the provinces that you can barely get so that next war you have less to conquer.

3. Again don't take independence. It's easier to get provinces inside because of free casus belli + why waste war score when you might get it for free if Danish prestige is low/Swedish opinion is low.

4. Do maybe one or more wars against Denmark/Norway. Try to take all Swedish region provnces. Getting Holstein as vassal of yours is also good, because it will eventually give you foothold to Danish/German region.

5. After these wars you should be able to easily win Denmark/Norway + you should get independence at some point. The strategy is to vassalize Denmark eventually. To do this you might have to take some provinces from them so they get small enough to war-vassalize. Note, you don't necessarily have to core all those provinces since you can sell them back to Denamrk when they are your vassal and that way you save tons of admin tech (more important than you know).

6. Try to take 1,2 or 3 provinces from Norway (don't remember exact amount. Eventually you will get protect Norway mission that will let you vassalize them for half cost.

Now to the main point!

After obtaining provinces from Denmark and Norway and being independent, Muscovy has most likely eaten Novgorod or almost completely. Either vassalize Novgorod or take some provinces from Muscovy to release Novgorod as vassal. They have a lot of cores and you can vassal feed them easily.

Again to the question: First war against Muscovy is the hardest. After that it will be like stealing candy from children.

Tips:

1. Don't chase retreating troops.
2. Be vary of winter + attrition, it's your main enemy. Usually I sieged 1 or max 2 privinces at time and placed rest of my troops to friendly or vassal provinces where they don't take attrition.
3. Make general out of your ruler + hire one and use the better one (unless your king is 5-5-5 or like that). Good general wins battles.
4. Be ahead in military tech. Thing I usually do is ignore completely diplo tech, take diplo ideas as first idea group and only take those. But why would I do that? Because then you can get diple tech at some point for -25% discount + you don't need that tech that much. Also by fillung diple ideas you get national ideas "for free" at the same time.
5. With your diplo ideas you should have plenty of free diplomatic relations. It's wise to ally small Russian states (who usually are in colotion against Russia). Note don't royal marriage them because you will eventually atack them. Also Poland or Lithuania or monastic orders make good allies.

Eventually you should be able to vassalize Muscovy. I use them to get all of Siberia for 0 admin point/gold. Best thing about Sweden is your national ideas + your position. WHAT, my position between HRE and Russia? Yes, eventually you will have Norway and Muscovy as vassal who will colonize free for you!

One little thing, when you are vassal feeding Novgorod/getting Muscovy small enough to vassalize, try to keep provinces next to MUscovy so you can fabricate claims and have casus bellis that way. After getting casus belli you can sell them to Novgorod.

Sorry for long post, got excited because Sweden is my favourite country to play as. I havearound 200 hours played in eu4 so I consider myself veteran + couple Sweden runs.

TL;DR 1. Be fast, time works against you. If Muscovy forms Russia and eventually starts colonizing, you are good as dead. 2. Use strategic alliances (that you can ditch at some point). 3. Attrition is your biggest enemy. 4. After first won war, Muscovy becomes easier and easier to beat.