There's little doubt in my mind that Jesse has the knowledge to "make the blue". The reality is that following a specific chemical synthesis actually requires very little knowledge of chemistry, particularly if you are following a straight up abstract and aren't trying to scale up or anything. Where the academic knowledge comes into play is understanding the terminology and procedures written in said abstract. If a step calls for distilling a liquid at a certain temperature and pressure, well then you need to know how to operate a vacuum pump, assemble a distillation apparatus, and have experience in the process from having the whole thing boiling over into your collection flask. The academics allow you to implement what is in the abstract, and the experience of doing it multiple times will usually result in higher quality yields as you get better at understanding the process. It's really no different than an advance form of cooking, and just like baking a cake 50 times, your 50th will likely be better than your first. Where the actual chemistry education comes into play is when/if something goes wrong, or doesn't look right, you have the ability to actually figure it out and/or correct it. Jesse/Todd are basically just replicating everything they've seen without any understanding of the process, which will work fine as long as their observations were accurate and nothing strays off course. Todd is basically making a minor error at one step, resulting in a lower yield. Assuming Jesse is familiar with this step, that's all it will take to get the Blue.
This might be overanalyzing things, but so far I've been quite surprised concerning the show's accuracy when it comes to the laboratory and chemistry aspects.