If you're using traditional +/- tolerances, a complete tolerance stackup isn't practically possible. Such tolerancing doesn't include effects of perpendicularity of holes, shape/form of holes, and a number of other factors, and these can have an immense impact. I've tried it on a chain of less than a dozen items, and it didn't yield anything realistic even if I included lots of gross assumptions about manufacturing capability.
If you're using GD&T, you can do a tolerance stack-up. It's a combination of graphical and mathematical work that accounts for worst cases (e.g. smallest dowel in the largest hole)of size, location, form, etc. It is quite comprehensive. This will give you the worst-case scenarios, not the probable case. Typically people will have some heart problems when they see how bad things could be, and rationalize that it never has been that bad, so the analysis is garbage. If you have hard statistical data on the manufacturing capabilities, you can greatly improve the results by including them in the calculation. There are a number of CAD analysis packages that do this, and you can always do it manually (that way you understand the process and are less likely to overlook something). My suggestion would be to take a good course from someone like Tec-Ease and work at it manually.
Hope that helps. Good luck!