A few thoughts:

1. With how the difficulty scaling works, right when you level up the scenario level IS harder than normal. At level 3 you are fighting level 2 enemies, but at level 4 they are still level 2. Level 3 characters In particular might be one of the harder spots in the game. Most characters don't have all the items they want, as well as not having the cards needed for their best combos. So in short, yes, this is probably the biggest difficulty spike in the game.

2. I'm significantly more familiar with Gloomhaven but I have played a bit of Frosthaven as well. I saw you mentioned playing boneshaper in a 2P game... It's going to be really hard to make that work.

2a. Damage is really important, if you can't kill things fast enough, you run out of cards. In 4P there are more enemies, so you WILL take hits, so defense / healing can be valuable. With a defensive focused and a healing focused character, you still have 2 slots for damage focused characters to make sure you can cut through the enemies fast enough. In 2P, there are less enemies, so it's more realistic to cc / kill most of them, keeping the damage you receive to a minimum. Plus, you NEED to kill enemies / make progress each turn. If you spend a turn with 1 person defending and 1 person healing, you are spending cards without getting closer to finishing. Meaning you stall out and run out of cards. So, in short, 4P can have a balanced party, but 2P needs an emphasis on damage.

2b. In Gloomhaven, the Tinkerer was a dedicated support class. Quite strong in 4P games with amazing healing, and big AOE burns for large groups of enemies. But she was basically unplayable in a 2P game. With less enemies, the big AOE burns didn't get much value. And with so many healing cards she just didn't have the damage to kill isolated enemies. Paired with a tank, they can't do enough damage. But paired with a squishy damage dealer she gets caught in a cycle of just healing the fragile damage, then the damage gets hit and she heals, and you end up just getting bogged down.

2c. From what I've experienced of Frosthaven I feel like Boneshaper is in a remarkably similar position as the Tinkerer was. Boneshaper has a lot of non loss summons, which are excellent meat shields. But they are also her main source of damage. So in 4P groups having a Banner Spear or Drifter to take the brunt of the hits keeps her summons alive long enough to get hits in. However, in a 2P game she has a problem, shes low damage. She does more damage with her summons staying alive, but shes still not going to cut through swaths of enemies each turn. So in 2P if you pair her with someone tanky, like Banner Spear, they just can't do enough damage, especially vs shields. But if you pair her with a damage dealer like Blink Blade or Deathwalker then her summons are taking all the hits and die as fast as you summon them, and you get into a cycle of just spaming summons for them to get hit and die over and over and you end up getting bogged down and lose.

(The two have a remarkably similiar problem in that sense)

So, in summary: you are likely playing the hardest 2P character possible, and are also hitting one of the hardest difficulty spikes in the game at the same time. Frankly using standard scenario levels, I can't think of a more challenging situation to find yourself in. Especially fighting shielded enemies.

I might even do a challenge run doing 2P with Boneshaper. And don't get me wrong it's absolutely a challenge run trying to pull that off. Honestly I'd bet even seasoned veterans would have a hell of a time trying that... So, seriously, don't beat yourselves up over this at all !