Not being safe to ever assume anything, it might be a good time to inquire if you are adjusting the headset with all of this spacer, handlebars and stem manuverings.
Sounds like you are a man (touching my ball, *giggle*). Yeah, you are right, when you are standing with your bike shoes riding over the middle bar of your bike. You crotch should barely not touch it. Means that bike fits on you if you have 5"9, a 54cm frame bike should be fine. You can go one size down (51 cm) , but not one size up (58cm), which does not fit you comfortably!
I took a look at the video and spotted this one on the sidebar
I like Lloyd and looked at some of the other fitting videos from GCN. I found it interesting when they suggest choosing the type of bike by having the rider touch their toes.
You can pick up gently used seat posts and stems from eBay for a fraction of their original price. You should buy a zero offset seat post, which will allow you to move your seat further forward.