No, you need to answer my question.
Copying inputs to outputs at anything less than 1 kHz is completely trivial. The question is - what do you really want to do in addition to mirroring inputs to outputs because I am quite sure you have something else in mind that you expect the Arduino to do but have failed to explain?
What is the significance of "for 3ms" in your question? Is the Arduino supposed to make some decision based on the duration?
Talking about interrupts is nonsense.
As a beginner, it is incredibly unlikely that interrupts will be useful to you.
A common "newbie" misunderstanding is that an interrupt is a mechanism for altering the flow of a program - to execute an alternate function. Nothing could be further from the truth!
An interrupt is a mechanism for performing an action which can be executed in "no time at all" with an urgency that it must be performed immediately or else data - information - will be lost or some harm will occur. It then returns to the main task without disturbing that task in any way though the main task may well check at the appropriate point for a "flag" set by the interrupt.
Now these criteria are in a microprocessor time scale - microseconds. This must not be confused with a human time scale of tens or hundreds of milliseconds or indeed, a couple of seconds. A switch operation is in this latter category and even a mechanical operation perhaps several milliseconds; the period of a 6000 RPM shaft rotation is ten milliseconds.
Unless it is a very complex procedure, you would expect the loop() to cycle many times per millisecond. If it does not, there is most likely an error in code planning; while the delay() function is provided for testing purposes, its action goes strictly against effective programming methods. The loop() will be successively testing a number of contingencies as to whether each requires action, only one of which may be whether a particular timing criteria has expired. Unless an action must be executed in the order of microseconds, it will be handled in the loop().
So what sort of actions do require such immediate attention? Well, generally those which result from the computer hardware itself, such as high speed transfer of data in UARTs(, USARTs) or disk controllers.
An alternate use of interrupts, for context switching in RTOSs, is rarely relevant to this category of microprocessors as it is more efficient to write cooperative code as described above.