The Tiny Core includes a (partial) hardware veneer that should make changing the "user timer" a bit easier. Give this a try...
#include <UserTimer.h>
void setup( void )
{
UserTimer_SetToPowerup();
UserTimer_SetWaveformGenerationMode( UserTimer_(Fast_PWM_FF) );
UserTimer_ClockSelect( UserTimer_(Prescale_Value_1) );
// Frequency is F_CPU / (1 * (0xFF+1))
// (8 megahertz) / 256 = 31.25 kilohertz
}
void loop( void )
{
}
The code changes timer 0 when millis is on timer 1 and vice versa.