[stefanos82]

Coincidentally, yesterday I had a chat with a friend that told me this very same case as yours.

His solution was

  - to replicate the whole layout of existing theme from scratch
  - produce the exact functional behavior of previous theme
  - on finish, he will simply going to get rid of the unnecessary plugins

It can be a bit intimidating, but if you know what you are doing, it will be worth the effort.