The chunks appear to be small rocks or pebbles that one collects in oily spots and crevices. They could have been knocked loose from the bottom of the bike or even fell into the case during an oil change and sat there until drained out. I'd try to crush one and inspect it closer if successful, if it turns to sand you know its not part of your engine.
As for the down shift to 1st from neutral, mine has refused a few times unless I pushed the bike forward or backward a bit; completing the downshift when you are still moving very slowly prevents being left in neutral. I find it happens to me but rarely and only when I'm absolutely stopped completely.
Tom, in Mountain Home, Idaho
2002 GL1800 (Illusion Red) Non-ABS, 128k miles
Retired Air Force
"Audentes Fortuna Juvat"