No idea why the if/elseif/else block above didn't work as intended... but I did get it to work this way instead... changes marked with <!--NEW-->
Code:
<variables>
<var name="MagicalDefense">None</var>
<var name="PhysicalDefense">None</var>
<var name="MDTElement">Neutral</var>
<var name="MDTModes">Firaga V|Stonega V|Waterga V|Aeroga V|Blizzaga V|Thundaga V|Banish V|Bio V|Diaga V</var>
<var name="MDTModes2">Flare II|Quake II|Flood II|Tornado II|Freeze II|Burst II|Holy II|Comet|Diaga V</var>
<var name="MDTOn">Aegis Schism</var>
<var name="MDTOn2">Carnal Nightmare</var>
<var name="PDTOn">Netherspikes</var>
<var name="Killswitch">Barbed Crescent</var>
<var name="Movement">None</var>
<var name="GearMode">Monk TP Gear</var> <!--NEW-->
<var name="MDTGear">Magical Defense</var> <!--NEW-->
<var name="PDTGear">Physical Defense</var> <!--NEW-->
<var name="TPGear">Monk TP Gear</var> <!--NEW-->
</variables>
....
<rules>
<if Spell="Autoset">
<if status="Engaged">
<var cmd="set Movement None" />
</if>
<else>
<var cmd="set Movement Move" />
</else>
</if>
<if Spell="$MDTModes">
<cancelspell />
<if spell="Diaga V">
<!-- Neutral element -->
<var cmd="set MDTElement Neutral" />
<!--NEW--> <var cmd="set GearMode $MDTGear" />
</if>
<else>
<!-- Stonega V, Waterga V, Aeroga V, Firaga V, Blizzaga V, Thundaga V, Banish V, Bio V -->
<var cmd="set MDTElement %SpellElement" />
</else>
<if advanced='"$MagicalDefense" != "None"'>
<var cmd="set MagicalDefense MDT-$MDTElement" />
<!--NEW--> <var cmd="set GearMode $MDTGear" />
</if>
<addtochat>Magical Defense Element: $MDTElement</addtochat>
<equip set="MNK-TP|$MagicalDefense|$Movement" />
<return />
</if>
<elseif Spell="$MDTOn">
<cancelspell />
<var cmd="set MagicalDefense MDT-$MDTElement" />
<var cmd="set PhysicalDefense None" />
<!--NEW--> <var cmd="set GearMode $MDTGear" />
<addtochat>Magical Defense: $MagicalDefense</addtochat>
<equip set="MNK-TP|$PhysicalDefense|$MagicalDefense|$Movement" />
<return />
</elseif>
<elseif Spell="$PDTOn">
<cancelspell />
<var cmd="set MagicalDefense None" />
<var cmd="set PhysicalDefense PDT" />
<!--NEW--> <var cmd="set GearMode $PDTGear" />
<addtochat>Physical Defense: On</addtochat>
<equip set="MNK-TP|$PhysicalDefense|$MagicalDefense|$Movement" />
<return />
</elseif>
<elseif Spell="$Killswitch">
<cancelspell />
<var cmd="set MagicalDefense None" />
<var cmd="set PhysicalDefense None" />
<!--NEW--> <var cmd="set GearMode $TPGear" />
<addtochat>Phys./Mag. Defense: Off</addtochat>
<equip set="MNK-TP|$PhysicalDefense|$MagicalDefense|$Movement" />
<return />
</elseif>
....
<!--NEW--><addtochat when="engaged"> Now Equipped: $GearMode</addtochat>