You wrote:

This transition seems abrupt...Although it might be more clear if I'd 
actually read the first two chapters :)

Yes it would be.  :-)  There are two stories going on here, one that 
takes place in the "present", and one that's a flashback to when they 
first met.  (The sentence "Kiyone couldn't believe it had only been a 
day since she'd met Mihoshi" should've been a dead giveaway.)  The 
two stories are joined together by Kiyone's memory and will come 
together at the very end, when Kiyone's recollection of their first 
meeting will inspire a way out of their predicament.

Sweat poured down her temples.  Her mouth was open in a continual
scream.  Her eyes looked ready to burst from their sockets.  Her hand jerked the
control stick back and forth so fast that it was a blur.

The description of Mihoshi's condition seems a little jerky...you might 
want to combine some sentences or at least not start three in a row with 
"Her <bodypart>".

Hmm.  It sounds okay to me (but then it would, wouldn't it :-) ).  
The sentences are meant to be jerky, in a way, to convey the jerky 
state Mihoshi is in.  It's meant to read in a staccato rhythm, boom, 
boom, boom!  At least, that's the idea anyway... :-)

------RM