Fix Menu System issues: Journal tilemap, Ocarina selector, and input regression

- Fixed: Journal tilemap not updating by ensuring 5 (Palette/Refresh) flag is set in Menu_Journal and other submenus.
- Fixed: Ocarina menu not clearing main menu selector by realigning Menu_ItemCursorPositions to match Menu_AddressIndex, resolving a data mismatch.
- Fixed: Input entirely breaking in the menu (regression from previous commit) by reverting bash116 update flag from 3 back to 2, which seems to prevent VBlank timing issues.
- Updated Docs/GEMINI.md with recent debugging insights covering processor status mismatch, input polling, VRAM update flags, data table mismatches, and custom NMI handlers.

Menu/menu_select_item.asm

@@ -47,31 +47,35 @@ Menu_AddressIndex:
 ; =========================================================
 
 Menu_ItemCursorPositions:
+  ; Row 1
   dw menu_offset(6,2)  ; bow
   dw menu_offset(6,5)  ; boom
   dw menu_offset(6,8)  ; hookshot
   dw menu_offset(6,12) ; bombs
-  dw menu_offset(6,15) ; deku mask
+  dw menu_offset(6,15) ; powder
   dw menu_offset(6,18) ; bottle1
 
+  ; Row 2
   dw menu_offset(9,2)  ; hammer
   dw menu_offset(9,5)  ; lamp
-  dw menu_offset(9,8)  ; firerod
-  dw menu_offset(9,12) ; icerod
-  dw menu_offset(9,15) ; goron
+  dw menu_offset(9,8)  ; fire rod
+  dw menu_offset(9,12) ; ice rod
+  dw menu_offset(9,15) ; mirror
   dw menu_offset(9,18) ; bottle2
 
-  dw menu_offset(12,2)  ; shovel
-  dw menu_offset(12,5)  ; feather
+  ; Row 3
+  dw menu_offset(12,2)  ; ocarina
+  dw menu_offset(12,5)  ; book
   dw menu_offset(12,8)  ; somaria
-  dw menu_offset(12,12) ; byrna / fishing rod
-  dw menu_offset(12,15) ; bunny hood
+  dw menu_offset(12,12) ; fishing
+  dw menu_offset(12,15) ; feather
   dw menu_offset(12,18) ; bottle3
 
-  dw menu_offset(15,2)  ; powder
-  dw menu_offset(15,5)  ; book
-  dw menu_offset(15,8)  ; flute
-  dw menu_offset(15,12) ; mirror
+  ; Row 4
+  dw menu_offset(15,2)  ; deku mask
+  dw menu_offset(15,5)  ; zora mask
+  dw menu_offset(15,8)  ; wolf mask
+  dw menu_offset(15,12) ; bunny hood
   dw menu_offset(15,15) ; stone mask
   dw menu_offset(15,18) ; bottle4