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There really is no clear cut answer to this. Based on my research there seems to be division among experts on the issue of whether or not removing knees poses harm to bald cypresses. There is even division on why the knees form in the first place - some say they only form in wet areas while others say the moisture is irrelevant. Is it moist where your tree is? Anyhow, according to the following extension article, "knees were once thought to be important in oxygen exchange for the roots but this notion has been discredited because researchers have cut away knees and trees have suffered no ill effects."

http://www.uaex.edu/yard-garden/resource-library/plant-week/bald-cypress.aspx

A bald cypress stressed by environmental conditions may respond by shedding its leaves - this is especially true in periods of long drought. I see that portions of Alabama are classified as abnormally dry right now.

For more information on cypress trees, please visit the following link:
https://www.gardeningknowhow.com/ornamental/trees/cypress/growing-cypress-trees.htm

If the branches are overly-long, then you can cut them back. The important thing to remember about cypress trees is to go slow and steady, branch by branch. This article may help you identify which branches to cut and how far back:

https://www.gardeningknowhow.com/ornamental/trees/cypress/cutting-back-cypress-trees.htm

Usually, you will want to harvest the seeds out of the cone, but if this was already open when you found it, then there are no seeds likely left in there. You should be able to see some if you pick apart the scales of the cone, if there are still seeds inside.

This article will help you grow these if you find that you do have some viable seeds that come up: https://www.gardeningknowhow.com/ornamental/trees/cypress/bald-cypress-information.htm

This is normal - it's the fruit of the bald cypress. Nothing to worry about.

There are some serious issues for you to consider as pointed out in the following article. Eventual size of the tree being a big one, soil acidity/alkalinity you can check with a soil pH meter or test kit from a local garden center. I'm not sure about cutting off the "knees", its best not to create wounds if you don't have to.

https://www.gardeningknowhow.com/ornamental/trees/cypress/bald-cypress-information.htm

The trees would benefit from a deep watering once a week, rather than two light waterings.

A common problem is chlorosis due to alkaline soils, especially if the tree came from acidic soil.

I would get a soil sample done (local extension agent can do that) and make sure all is well in the soil. You can also discuss the brownish tint as he is probably familiar with that in the area.

https://www.gardeningknowhow.com/ornamental/trees/cypress/bald-cypress-information.htm

http://edis.ifas.ufl.edu/pdffiles/EP/EP55700.pdf

https://plants.ces.ncsu.edu/plants/taxodium-distichum/