Sending Text File To Arduino Uno via COM Port

{
digitalWrite(13, HIGH);
delay(250);
digitalWrite(13, LOW);
delay(25);
}

I suspect your use of the delay commands is at the root of your missing characters. delay() is a blocking command that stops all further processing until it times out. At 9600 baud each character takes just 1 millsec to arrive and the arduino serial receiver buffer is only 128 bytes large, so you are bound to be overflowing the buffer.

I suggest you look over the arduino example sketch called blink without delay that shows a method to time events without blocking all processing, by using the millis() function.

Lefty