Code Talker has a lot of ways you can do it, and items aren't really that imported to it or most missions. It has two fully different ending segments based on your earlier actions, and a couple different approaches to the jungle and more so the mansion. Helps to use the southern cliff in the jungle and then the northern backdoor to the mansion, and then follow the river out of the jungle going west.
The parasite epidemic can be solved immediately upon contamination... it's sort of a puzzle I guess but there is a natural way to solve it on your own. Takes a lot of micromanaging though lol.
Metallic Archaea can be ruthless though. It's mostly just learning patterns.
Especially the CQC attacks, that you can learn to easily counter with CQC. But it can be relentless to learn the first time. It was by far the hardest boss or event in the game for me, too. I got my ass kicked a solid two hours, made worse by the fact that I brought Quiet with her NL tranquilizer gun and I wear wearing camo fatigues (which for video/headcanon purposes I wanted to get). Helps a lot if she has her fully upgraded anti-materiel rifle, and you're wearing heavy armour. Same with the rocket launcher: the FB MR with the larger ammo capacity helps a lot. Use the warehouse as a defensive wall to call in item drops if you need to switch.