Repeated measures, samples and control groupe

Hi all

Right I am struggling with understanding the concept behind some statistic when I deal with this problem; I have an experiment where I want to understand how long it take a fluid to reach a specific temperatur and how it effects its nutritional content when during a heating process. So from that I assume that "time" and "nutritional content" would be the response variabels. It is assumed that among other factors it will be interesting to investigate how these response variables change with three factors each with to level (factorial design). The warming process can not be performed without putting the fluid in a container and therefor it is different to measure the influence of these three factors without putting the fluid inside a container. However, it is also assumed that the container shape will influence the response variables depending on if it is shape 1 or shape 2. Therefor it is interesting to understand how these three factors varies depending on the container shape. Moreover, we know that the fluid we work with varies in terms of nutritional content and can therefor infiltrate the result if it is not considered.

How do I solve this problem?
* I am interested in knowing if the time is reduced and the "nutritional content" is increased when using shape 2 throughout all the levels of the three factors? Therefor I can not account the container shape as a factor, can I? It will be difficult to differentiate the influence of shape 1 and shape 2 in the factor "container size" on the response variables if I use it as a factor and investigate three factors instead of four? How should I else do?
* How can a control for the inherent variation in the fluid that I use, but that I am not interested in. I thought I could measure the nutritional content before the heating process and use it as control to compare it with the response variable "nutritional content" efter heating. But is this called repeated measure or paired comparison? And how to perform it?
* Should I consider blocking the experiment over two days would it involve performing the experiment two times? Should I instead repeat the run one more time?

I am really confused and hope some geniuses can help me out!

Thanks in advance