You're keeping too much. There's rarely a reason to keep more than a single stack of any crafting material. 99 is really rather a lot. It may not be enough to last you forever, but just replenish as you run out. Conversely, if you've only got one or two of an item and you're not going to be using immediately, sell it. Slots are too valuable to hold so few of an item. Sell your HQ materials. They fetch good money, and with good equipment and food and good technique, you should be able to HQ things without using HQ mats. Don't generally keep intermediate mats that you can make. Keep only the base raw materials and make intermediate mats as you need them.