interrupt and timer

Here is a problem I want suggestions:
I have some recovery after having detected some hardware failure. This recovery
is absolutely the most important thing I have to do, and dont want any
interruption.
So I want disable the interrupts during the recovery period.

The problem is that the recovery involve setting some internal registers to a
certains device, I can not access directly, instead I have to set a commands
register, activate the command, the read or write is completed until the device
ack'ed. Since I disable all interrupt, I poll the device to see if the device
acq'd. At the same time, I want setup a timer for the polling to prevent the
system hang. How would the timer would work if the interrupts are disabled?