Grammar, Usage / Rules for good comma placement throughout long sentences. [3]

proper comma placement

I'm trying my best to improve my writing. One substantial area where i always loose points is comma placement. for instance here is a small cutout of a paper where i was marked for improper comma placement.

Tools are not just physical items held in your hand. Not just limited to hammers and nails. Skills are tools of the mind. Just like their physical counterparts, shouldn't they be included in ethical consideration too? After all, the difference between a mason and a man making a giant mess is his ability to lay bricks properly. In many ways skills provide much more to the user than any physical item can ever hope to. Skills can be purely analytical, such the skills I'm building by going to college. Discovering new ideas that have given rise to tools such as differential equations and linear algebra. The pure logical building blocks to engineering.

Is my professor being difficult? When i play it through this website it sounds alright to me. Are there any particular rules i should follow?

readmytextto.me/share/8Hi7DT