if both engines have been repaired and both engines have exactly the same running problem, the only common denominator is the gasoline, or its delivery.
I had a similar problem recently, where my starboard engine run fine until I needed it to push the boat. The problem turned out to be a hole in a shared fuel line on the draw side- it didn't leak, but it allowed air to be sucked in while the SB engine was trying to pull fuel thru it. Kind of like if you put a hole in your drink straw above the drink, you'll get some liquid, but mostly air.
This may be your problem-- could be say, a pinhole or crack in the draw tube in the tank, or maybe the line right at the top of the tank next to a fitting. (my line was cracked next to a fitting, I found it by accident). You could be drawing enough fuel to keep it idling or doing short bursts, but not enough to feed it under any load.
If possible, bring aboard a separate fuel container, equipped in such a way that you can feed both engines from it, and see if the new fuel supply makes a difference. If it does, then you need to determine if your sucking air, or bad gas...
1988 SkipperLiner 53x14
1995 Tracker Party Cruiser 32 *for sale*
2003 Chaparral 260 SSI
2000 Allegro Bus 40' DP