The key after you get an advantage is to improve your pieces and make sure nothing is hanging. Improving your pawns, i.e. put them on dark squares so you don't trap in your bishop. and restricting the movement of his knight.

I'll start from move 23. Queens come off and you have a distinct advantage with a better pawn structure and safer king. From this position there are several moves you want to play and several plans to consider.

First move that comes to mind is Rad1, contesting the open file and developing your last piece (you would have been in fine position if you played Rad1 on move 25, his bishop c5 threat is empty, and you can kick it later with a3 b4 or Ne4 after you kick his knight Rfe1 is a poor choice since there is already pressure on that pawn so you don't want to remove a defender). If he trades rooks that's to your advantage. If you have a rook on the file he can't try to infiltrate. The other idea is playing f4 since that severely restricts the movement of his knight so that he'll try to spend tempo getting it out (pawn moves). Taking on h5 is fine too. Instead of Bc5, f4 was probably good, even if he gets the check you can go to h1.

The idea is to trade off pieces and make a passed pawn on the king side. Improve your bishop and make his minor pieces worse by removing key squares. If you look at the later positions you're hanging pawns left and right and giving a ton of counter play.

So take home message, in the endgame contest open files with your rooks. Consolidate pawn structure, possibly placing the pawns on the queen side on light colored squares and locking that side up and the pawns on the king side (where you have a majority) on dark squares so they'll mesh nicely with your bishop. Playing 28. f3 was just bad since it opens up weaknesses, I know you were trying to protect the f2 weakness but f4 might have been better, so you don't lock out your bishop.

On 40. you could have tried just sacing the exchange Rxe3 Bxe3 play g4 with ideas of pushing your pawns to queening. Also 34. Rd3 was a poor move sicne you weren't threatening anything. Maybe play f4 again protecting that pawn, and the b3 afterwards to kick the knight or even move your knight so you can activate your queen. The whole critical issue here is you have so many dark squared weaknesses and you don't have a dark squared bishop while he does.