Lauren: Thanks for the additional information. It sounds like what you are trying to accomplish practically is to determine key factors (you call them parameters) that influence a critical to quality process output characteristic (flow time). So if I were you I wouldn't focus so much on which prototypes are different...but which factors drive optimal performance in the critical to quality characteristic. Then try to figure out levels for the factors which optimize flow time, or in a perfect world, give you insight into key factors and levels that will be incorporated into a more formal DOE oriented approach to solving the practical problem at hand. This is the essence of using historical or happenstance data (this sounds like the type you have) to characterize process performance using empirically generated data TO INFORM DOE.
But it sounds like you don't have the luxury of going down the DOE path...if that's the case...
From the sounds of it your knowledge of modeling techniques based on using empirically derived data is fairly immature? A few thoughts for you at this stage;
1. Can you find someone to mentor you that has a background in empirical modeling with JMP or JMP Pro? They can provide you with specific guidance that you will hopefully find valuable.
2. Take a look at some of the JMP On Demand Webcasts available at :
On-Demand Webcasts | Mastering JMP
Building Better Models | JMP
You may find the empirical modeling and exploratory data analysis focused presentations informative for the type of problem you are confronted with.