about component made by user logic

To change the debug options just open the software projects you have created and modify that from there. To change the level of the debug module you have to do that in the NIOS II core itself (double click it in the GUI).

But I think the first thing is to determine whether it's software or hardware causing this (depending on what you do, just blame the other hehe). Are you able to build the hardware with your custom peripheral and run lets say "hello world"? (if this doesn't work then I believe your problem is a hardware issue).

In the case it is hardware related check out the results from the timing analysis (fmax and slack times). I've managed to have designs fail that barely clear fmax due to signal jitter, maybe this could be a problem with your design.

Unfortunately I'm not sure if I can think of anything else unless you find more information that you can provide.