No, I was not referring to the Velocity check; that part is fine, it's the line above (544) that was wrong, which you have corrected. You should have no problem adding the Velocity rule back in, if you wish to.
Namas Arrow|Refulgent Arrow|*Arrow is redundant; additionally, unless you change 540 to also include Refulgent Arrow, it will not reach line 544 and will default to the "WS Base" set. That is, unless you just got rid of the other rules and replaced it with your aforementioned code.
This should work (lines 540-559).
Code
<if spell="Coronach|Namas Arrow|Jishnu's Radiance|Last Stand|Wildfire|Refulgent Arrow">
<if spell="Last Stand" TPGT="299">
<equip><lear lock="yes">Auster's Pearl</lear></equip>
</if>
<if spell="Coronach|*Arrow|Jishnu's Radiance|Last Stand">
<if spell="Namas Arrow|Coronach|Last Stand" BuffActive="Velocity Shot"><!-- Velocity Shot WS Body Rules -->
<equip when="precast|midcast"><body lock="yes">Sylvan Caban +2</body></equip>
</if>
<equip when="precast|midcast" set="%Spell-$VAR-WS" />
</if>
<elseif spell="Wildfire">
<if Mode="OR" Day="Firesday" WeatherElement="Fire"><!-- Wildfire Obi Rules -->
<equip when="precast|midcast"><waist lock="yes">Karin Obi</waist></equip>
</if>
<equip when="precast|midcast" set="%Spell" />
</elseif>
</if>
<else>
<equip when="precast|midcast" set="WS Base" />
</else>