@Andriy242 I would try removing the completed save and let the game boot up the prologue without loading into another save first, as a modified gameconfig can cause the game to crash when starting a new game from a loaded save.
So I did something very similar actually to what you mentioned. I even cleared all the rockstar folders from Documents to make sure everything was gone, but here is what I eventually had to do to fix the problem.
Went to My Documents and Deleted the profile from the GTAV folder and not the Launcher Folder.
Loaded GTA5 and crashed with a VCx64 error code, so that told me that VC was not initialized.
Reinstalled VCx64, rebooted the computer
Checked to make sure the GTAV folder in My Documents had no Profile folder.
Loaded up GTA5, and pressed Story mode and it went into Prologue.
So far have run it for about 5 hours and no issues and no performance drops.
*With this I was able to start story mode from scratch, have all 2000+ addon vehicles available if needed, replaced cars in traffic, etc. No issues with crashing.