Code:

#include <avr/io.h>
#include <avr/wdt.h>
#include <avr/interrupt.h>  /* for sei() */
#include <util/delay.h>     /* for _delay_ms() */

#include <avr/pgmspace.h>   /* required by usbdrv.h */
#include "usbdrv.h"
#define F_CPU 16000000

uchar pres,prev,mask,ind[4];
short int ch1,ch2,ch3,ch4,chf1,chf2,chf3,chf4;
short int dataBuffer[110];  

/*=============================================================================
                Timer2 Interrupt routine
=============================================================================*/

ISR(TIMER2_COMP_vect)
{
   sei();
   ch1++;
   ch2++;
   ch3++;
   ch4++;
   
}

/* ------------------------------------------------------------------------- */
/* ----------------------------- USB interface ----------------------------- */
/* ------------------------------------------------------------------------- */

usbMsgLen_t usbFunctionSetup(uchar data[8])
{
  
  TCCR2=0;
  TIMSK &=!(1<<OCIE2);

usbRequest_t    *rq = (void *)data;


    if(rq->bRequest == 0)                 /* echo -- used for reliability tests */
    {       
        dataBuffer[0] = rq->wValue.bytes[0];
        dataBuffer[1] = rq->wValue.bytes[1];
        dataBuffer[2] = rq->wIndex.bytes[0];
        dataBuffer[3] = rq->wIndex.bytes[1];
        usbMsgPtr = dataBuffer;          /* tell the driver which data to return */
    return 4;
    }
    
    else if(rq->bRequest == 1)         /*reset and restart timer by host request */
    {
        
        ch1=ch2=ch3=ch4=0;
        ind[0]=1;
        ind[1]=26;
        ind[2]=51;
        ind[3]=76;
    
    
        TIMSK|=(1<<OCIE2);      /*enable compare match interrupt*/
        TCCR2=0x09;            /*start timer with no prescaler, CTC mode*/ 
        TCNT2=0;                 /*Clear timer count*/
        TIFR&=!(1<<OCF2);
        PORTB&=!(1<<1);
    return 0;
    }
    
    else if(rq->bRequest == 2)
    {   
    dataBuffer[0]=ind[0];
    dataBuffer[25]=ind[1];
    dataBuffer[50]=ind[2];
    dataBuffer[75]=ind[3];   
        usbMsgPtr = dataBuffer;         /* tell the driver which data to return */
    PORTB|=(1<<1);
        return 200;                       /* tell the driver to send 200 bytes */
    }
    return 0;   /* default for not implemented requests: return no data back to host */
}

/* ------------------------------------------------------------------------- */

int main(void)
{
uchar   i;



    wdt_enable(WDTO_1S);
    /* Even if you don't use the watchdog, turn it off here. On newer devices,
     * the status of the watchdog (on/off, period) is PRESERVED OVER RESET!
     */
    usbInit();
    usbDeviceDisconnect();  /* enforce re-enumeration, do this while interrupts are disabled! */
    i = 0;
    while(--i){             /* fake USB disconnect for > 250 ms */
        wdt_reset();
        _delay_ms(1);
    }
    usbDeviceConnect();
    
    sei();
    OCR2=0x78;         /* set compare match value  */
    
    
    DDRC=0xf0;
    DDRB=0x3f;
    DDRD=0xeb;
    prev=PINC;
    ind[0]=1;
    ind[1]=26;
    ind[2]=51;
    ind[3]=76;
    for(;;)
    {  
      /* main event loop */
        wdt_reset();
        usbPoll();
    
    pres=PINC;
    mask=( prev ^ pres ) & pres;    /* rising edge */
    if(mask) 
    {
      TIMSK&=!(1<<OCIE2);
      chf1 = ch1;        /* Freeze all the counter value upon transition detection*/
      chf2 = ch2;
      chf3 = ch3;
      chf4 = ch4;
      TIMSK|=(1<<OCIE2);

      if((mask & 1) && (ind[0]<25))
      {
        dataBuffer[ind[0]] = chf1;
        ind[0]++;
        ch1=0;
      }
      
      if((mask & (1<<1)) && (ind[1]<50))
      {
        dataBuffer[ind[1]] = chf2;
        ind[1]++;
        ch2=0;
      }
      
      if((mask & (1<<2)) && (ind[2]<75))
      {
        dataBuffer[ind[2]] = chf3;
        ind[2]++;
        ch3=0;
      }
      
      if((mask & (1<<3)) && (ind[3]<100))
      {
        dataBuffer[ind[3]] = chf4;
        ind[3]++;
        ch4=0;
      }
    }
    prev=pres;
    }
    return 0;
}

/* ------------------------------------------------------------------------- */