Welcome to the community. I don't know if I have a complete understanding of your situation, but here are some of my thoughts:
1. If the level for Solvent is dependent on the level for Aliquot Volume, then Solvent is nested in Aliquot Volume (expressed Solvent[Aliquot Volume]) If it is truly nested, there will be no interaction estimable.
2. Perhaps you could look at those two factors as one combined factor which would have 2 levels of the ratio of solvent to volume (e.g., 25/4 and 100/1600). If this factor is the most active, then understand appropriate ratios in a subsequent design. This is a screening design, so expect to iterate.
3. I'm not sure why you consider Prot time and Prot temp as categorical? Those values appear to be continuous. Granted "Overnight" is vague, but it is some quantifiable number of minutes.
"All models are wrong, some are useful" G.E.P. Box