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The reason why you can only use UART 1 is because according to MCU API, UART 2 is used as Linux kernel console and you have to stop this service in order to use it.
Also according to MCU API, UART parameters cannot be changed, so in that case the packet length is 8 bit. So make sure you are expecting this amount of bits and that you have set the baud rate correctly.
Regarding timer interrupts, they are not mentioned at all in the MCU API, so they are not currently supported.
I understand your concerns with the current limitations of the Edison's MCU, nevertheless, Intel is constantly working on improving their products but we will have to wait for a new version of the MCU's API that hopefully increases the features available, however there's not ETA on it.
Thank you for your answer! It was more a moan when a question - it is pity that powers of this MCU are hidden from us.
I can hardly remember last time when I used UART settings different from "8 bits, 1 stop bit, no parity" , I think it was than I was a student.
What about MMU and Viper OS? Maybe I can address peripheral registers directly? I guess no but...
Looking forward to get more powerful API that matches MCU functionality or to get bare-metal access to MCU.