Just to go against the earlier advice on weapon/acc upgrades I'd say go ahead and mess around with it. You will have the opportunity to get a lot of money later on, in the 11th and 12th chapter, and it will allow you to do a lot more, but the lower levels of items are extremely cheap in comparison to the later ones. Also, you really aren't wasting anything. It's a completely replaceable resource. I personally found the boosts to my stats very useful. Remember to try to get a good multiplier (3x preferably) by using natural components, then spend your mechanical components for extra points. There are specific components that will net you more points than others but I couldn't tell you what those are in English.
Yes, money can be tight for most of the game, but I really don't think you're wasting anything by experimenting with weapons. Items serve no other purpose. (Other than sale, and again those are very obviously marked.) It should be fairly clear what stat each weapon prefers and what extra bonuses it confers. Messing around with it costs you nothing in the long run.