There are a number of different tools/approaches that might be helpful for this kind of problem. Which ones work best for you will be a matter of personal preference.
You could do all of this with the built in query-replace-regexp, bound to C-M-% by default. Searching for "(0.[[:digit:]]+)" and replacing it with "(\1)" will start an interactive search. You can then press 'y' for each number you want to wrap in parentheses, and 'n' for each number you want to skip. That's probably the quickest way to solve the problem you describe.
For more general approaches, you might consider:
Wrap region makes it easy to quickly "wrap" a region with delimiters, including (), {}, "", and extendable to include pretty much whatever you need. It can also be tweaked so that different modes will apply a different suite of wrappers.
Expand region makes it easy to quickly select a region. With point on a word or number, expand region makes it easy to select that word, then the sentence, paragraph etc. This also works in code, where you can quickly select the object at point, then the expression, then the containing function etc.
Expand-region combined with wrap-region is a good way to wrap individual numbers in your text. You could use keyboard macros to repeating this for multiple numbers. Keyboard macros let you 'record' a series of key presses, then 'replay' them. In this case, you could record the keypresses that mark your number, wrap it in parentheses, and then move to the next number. Stop recording, and then repeat the macro over and over until you've wrapped everything you want.
