Parasite Eve inventory management

I've just gotten around to playing the PSN edition of Parisite Eve I downloaded almost a year ago. As you know inventory management is kind of tight in this game and I am really not sure what I should be giving priority to.

For instance I just had to clear some 'Junk' out of my inventory to make room to pick something up. Which has me wondering, is Junk really just uselessly cluttering up my valuable backpack spots? Or is it something that having not collected them all through the game will screw me come the last dungeon?

Does anyone have any tips on what I should be keeping/chucking and what is the best strategy for parceling out upgrades? I'm sure I can find lots of step by step walkthroughs on how to play the game, but I am just looking for some general guidelines on not screwing myself over in the long term.

P.S. I really dislike games that let you screw yourself by not being psychic and predicting on what the developers thought was important to keep/upgrade/spend money on.

I'm regretting not having played Parasite Eve in a long time now. I can't remember exactly what Junk is used for, but I don't think you'll screw yourself by getting rid of a piece here or there. I know there's a special powerful weapon you can get if you collect 300, but it's not remotely necessary to do.

As for upgrades, I seem to recall that later in the game you can use old weapons to improve the stats of new ones, so you don't completely lose upgrades by using them on less powerful weapons early on. I don't remember having any real problems when I first played through the game many years ago, and I'm sure I was not playing as efficiently as I could at the time.

Speaking of Parasite Eve though, I was having the urge to play it again soon. Such an awesome game, I might have to start another playthrough soon.