Published manuscript to handbook or manual
would it be against the journal policy if I do this?


It is not against journal policy for


  a handbook/manual [to be] based on...published methods in a...journal. 


Indeed, anyone is free to write a handbook/manual based upon published materials. (Such a handbook/manual should not plagiarise, of course, and the OP has noted that the handbook/manual differs in content, format, structure, and style. Furthermore, the OP notes that the original sources have been cited.) Regarding, 


  we borrowed and cited some of the figures


You need to check this is permissible, it has been answered elsewhere on this site.

There may be other concerns, but the question doesn't raise them.

TL;DR: Write your handbook/manual as-if you didn't write the original sources.