You can try extensions such as TIG's Solid Solver and ThomThom's Solid Inspector2 and CleanUp3 however if your model is as much of mess as you imply, they will likely not be able to fix everything. Probably there will be things that will require human decision making to repair.
It doesn't help you now but if you know that a 3D printed model will be required it would be best to model that in mind from the beginning making sure that all bottom groups and components are reported as solids. Solid groups and components tend to be cleaner and are easier to work on so there's additional benefits to making solids from the beginning.
You don't have to collect all of the groups and components into a single solid for printing, either. As long as all of the objects are solids, it should print fine.