Removing the guns from the B-29 for low-level missions

I've read in numerous accounts where the guns were removed from the B-29s once they switched to low-level, nighttime, incendiary missions.  I have four volumes of Chester Marshall's The Twentieth Air Force anthology, I've read them religiously since I was a child.  I can't recall or find a single account of what the gunners did without their arms.  So my question is this:  If the guns were removed, what purpose did the gunners serve?  Were all guns removed?  Did the tail gunner retain his guns?  Were the guns removed for the mining missions over the Shimonoseki Straits? 
Unfortunately, the government tells me that my grandfather's records were affected by the fires at the gov't archives, so I cannot obtain many documents relating to his service.  But, I do recall him telling me, and also seeing the documents (as they were produced on Tinian) that accounted for him being credited with destroying 3.5 fighters.  (Very exciting descriptions and details, I wish I could get my hands on the verbatim accounts).  If his squadron didn't start their missions until 25 February (roughly?), and were suddenly thrown into the low-level technique ( him and his crew earning the DFC on 10 March '45 for their role in the infamous Tokyo Firebombing), how did he, as a relative newcomer, find time to earn credit for 3.5 Japanese fighters destroyed, if he functioned without guns through the remainder of his missions?  Is it likely he (and others) inflicted much more damage (than documented) against the Japanese fighters?  Is it so true that it was difficult to get confirmation of 'kills' and that is why there are so few gunner 'aces?'