How to delay clock in real hardware?

I feel like you are maybe asking the same question which FvM answered here:

http://www.alteraforum.com/forum/showthread.php?t=43082&p=178215#post178215

Since you are saying you have 1000 step counts, you may want to do something like:

output(0) = turn on at 0, stay high for <pulse_width>

output(1) = turn on at 250, stay high for <pulse_width>

output(2) = turn on at 500, stay high for <pulse_width>

output(3) = turn on at 750, stay high for <pulse_width>

If this is not what you want to do, maybe post simulation waveforms that describe what is wrong.