My thoughts with the limited description of the situation. I apologize if I've completely misunderstood your inquiry.
You have a measure on a part before assembly and after assembly in a tool. Do you know the precision of the measurement device? Is the measurement on the same location on the part? If you have not studied and separated these components, then the components of all of the variation in your study is a combination of part-to-part, tool-to-tool, within part and measurement (and associated variables at each layer). You do potentially have multiple measures within tool, but those are confounded with the assembly process variables.
Ways to look at your data include:
1. Multivariate Methods>Multivariate
2. Control charts with a subgroup size of 2 (the before and after measures). This would put the part-to-part, within part and measurement variability within subgroup and then plot the averages (due to tools).
3. Graph Builder...many options to show what you might want (dependent on the user).
4. Fit Model for some quantitative analysis
"All models are wrong, some are useful" G.E.P. Box