Hello Dobrica,
I think you have done well to get your timer running.

If I read 'between the lines' you now need to receive serial data (but to correct you) without your timer loosing time.

The only viable method is to base your timer on a fixed rate timer interrupt. The overhead in processing the interrupt and rippling the timer count would be minimal. The serial receive could also be interrupt driven.

Don't be put off by the initial complexity of issues to use interrupts. They are a powerful tool in a software developers toolkit.

Graham