If you are missing dependencies after decompiling the entire jar, that could mean the jar did not include them. When you create a jar, you can choose not to include dependencies in it, but this assumes that they will be available on the classpath at runtime. Check if there are any relationships with other jar files on the classpath when you run the original jar. See this answer for details on how to achieve this. Once you have identified all the dependencies, you can easily compile the jar from an IDE such as IntelliJ/Eclipse or from command line.
As a side note, if the changes you would like to make to the jar are minor or isolated I recommend editing the bytecode (much easier for small edits). I prefer this bytecode editor.
If decompilation fails on some parts of the code, the functionality of the jar will not be restored upon recompilation. In this case, instead of going through all available decompilers and hoping that you can decompile that code, I suggest you identify the set of classes which you are trying to edit, modify the rest of the classes such that they compile and do not have any side effects on the classes which are of interest to you (do not delete anything that is referenced by these) and compile the jar (even if this isn't the jar you want). You can then extract only the class files which you wanted to modify from the jar, and overwrite them in the original jar. This will only work if your changes didn't have any side effects.