cmalley143 Hi
Having reviewed, The custom.css file located at /templates/ja_university_t3/css/custom.css
shouldnt have any adverse effect from the CSS added in specific file for specific elements as shown in screenshot as there isnt any CSS seen targeting them
In regards to your specific queries:
a) Try add this to custom.css file and adjust margin value accordingly :
#t3-content .eb-container .eb-category-description table ul li{margin-left:10px !important;}
b) Change span here - <div class="right span11">
to <div class="right span10">
Code in reference -
<div class="right span11">
<h3>These are the required course books. </h3>
<p>If you do not have access to these books for class, you will need to purchase one below. <a href="/files/books/amls_reg_book.jpg" target="_blank" rel="noopener noreferrer"><br></a></p>
<p>ISBN 9781284180343, 2020 9th Edition, 736 pages</p>
</div>
c) Try add this also to custom.css file :
#t3-content .eb-container .messagetop{margin-left:0 !important;}
Kindly ensure to clear your browser cache if changes dont reflect.