Gem/Rune Storage - I know it wasn't done before HUv1.3, and I don't expect it to have been done afterwards. One feature of v1.7 that kinda helps Rune management is that there are several cycles where a rune is equivalent to another rune, so tossing one of them into the cube and transmuting returns the alternate rune. Out of the 31 runes, there are about 12 equivalent to another, and it is possible to buy four runes per act (stopping at Lem in A5), so I'd expect players to be pretty comfortable either keeping just 1-2 of runes that they could transmute into their partner rune, or maybe just buying them. That aside, a GemBox sounds fun, I'd recommend trying v1.7's system for now (works well enough for me), and if folks would like a GemBox for v1.8 and v1.9, then it sounds like a great improvement to look forward to.
Unique Suggestions - I'm of the opinion that until we share a link to download the polished version of v1.7, then you're welcome to recommend items. Here is a link to every
HUv1.7 Webpage produced by the WebPageMaker (a more advanced program than currently available in the Homemade Modification forum). It will take me a while to prepare a test package, if I need to, but it's easy for me to share these webpages. The main reason I disabled most of the uniques in v1.3 is because once I'd rebalanced some of them for v1.7 they seemed kinda plain, and occasionally I'd wished that they had dropped as a triple durability Rare item instead, so I disabled them and only added uniques when they seemed like a good idea (Some basic items might still seem boring).
One significant feature in v1.7 is upgrading items from Basic to Exceptional and Elite. I made those recipe ingredients more common, and the upgrade will add +Skills or PDR/MDR for item types where the level increase justified it (typically an Exceptional is 35-40 levels higher than its Basic type, while nearly all Elite items are between levels 80-90). The upgrade recipe for every equipment type is to cube an item with 2 (Basic) or 4 (Exceptional) StarStone gems and AdamantHammer. One reason this system works well enough is because all unique weapons and armor have the same +% mods from tier to tier (I wanted +100% to be as important to a level 9 character as to a level 99 character).
With that in mind, are you sure you want to wait until char level 90 before using your Legendary Mallet unique? It's no problem creating it as a basic or exceptional version (The only difference is that Elite would have +3 skills, the exceptional +2, and Basic +1, literally nothing else in your suggestion would be changed).
For now, I understand that you'd like a blunt weapon (+50%DmgUndead automod) with max sockets (i.e. its strength is versatility), and below average physical damage and speed (i.e. the balance for its strong point).
For now, I'd implement it this way:
Unique War Hammer+1 All Skills (Standard on all 1-H weapons after level 33ish, +3 as Elite)
5 Sockets (current max for 1-H weapons, 5 ith Runes would be another +100%ED, 5 excellent jewels could add +60%IAS with +50-80%ED with more)
+55-66% EnhancedDamage (standard range is 85-100%)
+50% Damage to Undead (hardcoded automod on blunt weapons)
I could try adding a negative IAS mod, but I think it would be ignored even if the text files say they would allow it (e.g. negative %ED was ignored even when I'd try to set it up as acceptable). War Hammers happen to be slow anyways, so it'd probably be fine as it is.
Take a look at the white weapons webpage and let me know if the automods of another weapon class appeal to you more.
P.S. If you want to interact with the Prefix and Suffix webpages, then don't use Chrome (it has a bugged implementation for hiding table rows), and allow JavaScript (when you select a level and item type, the script will filter out invalid rows from the table, and will collapse those rows unless you're using Chrome). If you have to use Chrome, then after filtering, just search for text "group" since that only appears once per unhidden row.