First thing I would up grade is the yellow springs, then print with your printer for awhile before changing anything else.
I wouldn’t recommend XS tubing, I only use the TL. If your filament gets a little out of spec it will jam in the XS tubing because of the super tight tolerance.
Since no one else seems to have noticed, the physical bed size of the Ender 3 is 235x235. I would stick with your glass bed and maybe later upgrade to a flex steel plate. Creality makes a good one (have it on my Ender 3), there is also Wham Bam which works great but is more expensive.
You don’t need an enclosure to print PLA or PETG, but make sure draft aren’t hitting our printer or you will get failed prints.
Octoprint is great if you are doing long prints and you are out of the house for a long period of time and you want to keep tabs on the print.
For filament storage, I use round plastic containers from the dollar store. I put some desiccant packs in the bottom, throw in the roll and put on the lid. I have about 25 of them stacked up in piles.