So far I can't see anything obvious. I note that you are doing analogRead inside an ISR, so the time left (with interrupts enabled) is now down to 900 uS or less. Still, with serial interrupts every 87 uS that shouldn't push you over the 900 uS limit. Can you time (eg. with strobing pins and a logic analyzer) exactly how long the ISR takes? Maybe it is a lot longer than you think.
How do you know you are missing the ticks?