You might want to consider turning the difficulty right down, which will let you charge through easily. You can also use cheats to make things easier. Just turn it back to your normal level before you level up if you play on core rules or above, or you'll be getting too many hp.
I'm afraid that afaik there isn't a save editor which can alter what quests you have and haven't done, but you can quite easily use Shadowkeeper to give yourself the items, xp and gold of your other party, and just avoid talking to the quest givers for the quests you didn't do. In effect you'll then have done them.
You'll still need to go through Durlag's to trigger, say, finding Dalton, but as I said above you can use cheats to speed things up. I believe they're enabled by default on the GOG version, but if not then just edit the ini to add cheats=1. Then you can use console commands to speed things up, which you can find in several places online, like here
. You may find the move location code particularly useful, as you can go straight to the final level. The code for the area is AR0514, though I'm not sure where exactly in the area it will spawn you. Make sure you pick up the appropriate quests you haven't cashed in before starting!
Then the only thing you'll then be missing is journal entries, which I'm afraid I can't help you with. They aren't that essential, though, as they're only the ones for the done quests, and they'll be wiped if you plan to proceed to BG2 anyway.
So, in summary, you should:
Turn the difficulty down to minimum
Load (and don't overwrite!) the latest save you have without the issues
Pick up the quests that are unfinished in your corrupt save
Use the cheat console to skip to the final area of Durlag's Tower
Complete that area, which shouldn't take too long with the lower difficulty and knowledge of how to solve all the puzzles
Save your game in a new save slot
Open your new save in Shadowkeeper, and your corrupt save in the game
Copy the inventory differences, gold and experience into your new save (which may be quicker if you sell items you plan to sell first)
Save in Shadowkeeper, and load in the game, and you should be able to progress as usual
Oh, and don't forget to turn the difficulty back up to your normal level when you're done! If you find that you're having trouble, say with the Durlag's Tower boss, you can edit in the items your corrupt save has at that point to make things easier.
I know it looks complicated, but it shouldn't take all too long: no more than an afternoon, in comparison to the time you'd take going all the way through TotSC again.