How to add additional millisecond delay to microsecond delay generator
You could count timer compare matches.  The following illustrates the principle, maybe not accurate as written but I am sure the counter loop will be precise enough for your needs, considering you want to use an Arduino.  Depending on the time resolution you want, you may be able to run other code while the software counter is active.

The following can count to several seconds, depending on values of OCR1A and counter_target.

unsigned int state, pulse_delay;
byte counter[3]={0,0,0}; // 24 bit counter, you can make it longer in principle

byte counter_target[3]={0,0,0}; // defines length of delay you want

void setup(){
state=0;
TCCR1A=0;
TCCR1B=0;
}

void loop(){
switch (state){
case 0: // idle state machine // you other code here
counter_target[0]=0; // For example
counter_target[1]=0;
counter_target[2]=1; // corresponds to (1+65536)*pulse_delay/clock_scaler
// when you are ready to start counting
state=1;
break;

case 1: // setup timer
counter[0]=0; // Zero the 24-bit counter
counter[1]=0;
counter[2]=0;
OCR1A = pulse_delay; // number of pulses to count = 1+OCR1A
OCR1B = OCR1A+1;
ICR1  = OCR1A+1;    // Just to make sure these don't cause compare match 
TIFR1 |= (_BV(ICF1) | _BV(OCF1A) | _BV(OCF1B)); // Clear match flags
state=2;
TCCR1A = B00000011; // Fast PWM mode 15 on UNO, OCR1A=TOP
TCCR1B = B00011001; // Clock prescaler 1
break;

case 2: // Counting up
loop_until_bit_is_set(TIFR1,OCF1A); 
TIFR1 |= (_BV(ICF1) | _BV(OCF1A) | _BV(OCF1B)); // Clear match flags
counter[0]+=1; // Increment counter by 1
if(counter[0]==0x00){counter[1]+=1;
if(counter[1]==0x00){counter[2]+=1;}} // etc

if(counter[0]==counter_target[0] &amp;&amp; counter[1]==counter_target[1] &amp;&amp; counter[2]==counter_target[2]){state=0;}  // Check if we have reached the target delay
break;

}
}