Each player should have their own yml file for storing their Parkour data, this includes combining their entries in the players.yml and inventory.yml.
This will follow the same pattern as session files, but "/Parkour/player/(UUID).yml".
This should have a major impact on performance as writing to the existing yml files with 100s of entries would get considerably worse as more players use it.
With this means a rewrite of how ParkourRanks are stored, currently stored as "ServerInfo.Levels.(level).Rank", which is bad. Not sure of where / how to store this yet.

This would require a quite large converter task, but the "PlayerInfo" ConfigurationSection in players.yml can be ported over fairly easily.

This has been implemented in the pending 7.0.0 release.
Each Player will have a JSON created in /Parkour/players/(ID).yml.
The (ID) value can either be UUID or Player name, which can be configured in the config.yml.