My first suggestion is that for custom items, if it's under the "Whistle" Class, then one of the Miscellaneous attributes should be the sound effect number that plays when you use the item. This way, the default whistle can be the short whistle song but you can have other "Whistle" items that actually play other instruments (Perhaps an ocarina that plays the "Song of Time")

Secondly, since we can now have custom items, such as various levels of hammers, new swords, and so forth, there should also be a way to have flags that require you to strike them with custom items. Here's how I propose this be done.

In the tools->Flags menu, there should be 10 new flags (#98-#107) called Custom Item 1, Custom Item 2...Custom Item 10. Now, each of these custom item flags can also have a secret combo. So, in the data->secret combos menu, there should be a new tab called "Custom Items" and under this new tab it would have secret combos for Custom Item flags 1-10 (flag #98-#107).

Now, in order for a custom item to trigger these flags, you would go into the item editor. When you pick an item to edit, there should be a new tab called "Flags". Much like the 4 weapons under the "Action" tab, there would be 4 drop-down menus for Flag 1, Flag 2, Flag 3, & Flag 4. In other words, it allows you to assign up to 4 flags that the weapon can trigger.

Some examples:

The default flags for a wooden arrow would be: Flag 1-Wooden Arrow, Flag 2-None, Flag 3-None, Flag 4-None

Since the silver arrow triggers both silver arrow & wooden flags, the default flags for these would be: 1-Wooden Arrow, 2-Silver Arrow 3-None 4-None

Likewise, the golden arrow triggers all arrows up to & including golden arrows: 1-Wooden Arrows, 2-Silver Arrows, 3-Golden Arrows, 4-None

You could now make a "Fire Arrow": Flag 1-Wooden Arrow, Flag 2-Burn, Flag 3-None, Flag 4-None

You could have a custom Bomb that sets off it's own flag: Flag 1-Custom Item 1 flag. Now, for everyone Custom Item 1 flag (flag #98), it could be triggered by this custom bomb (like a mega bomb, or Ice Bomb, or something) And you'd need to select the appropriate secret combo as well.

Now, let's say you wanted to make a level 2 Wand required for your game. You would edit a new item so that it's in the Wand class, with a level of 2. Then you would go into the "Flags" tab and set it to one of the Misc Flags, giving it something it can trigger. You could also set a second flag so that it also triggers the original Wand flag, making this item a true upgrade, much like the silver & gold arrow examples.