You're not the first to say it's slower after installing V2, but I see no such effect on my computer, except a one-time delay on startup as map.rwm is generated. As there is no new functionality since 0.81a I don't know what could cause a further slowdown (EB is slow from the outset due to lots and lots of code).

You don't need to delete map.rwm again. The file is a compilation of a lot of other game files that the game uses often, probably for faster reference. When you change certain stuff in certain files, you need to delete it so the game can become aware that there's new data instead of referencing old stuff that no longer exists, leading to crashes.