[4RE KLR]

I agree with MR Mustang, mount the box inside out of the heat and it will work better. I had a similar problem with an old truck i had and it was the MSD box.

Question:
You said you were running it hard, or something to that effect. If it is a MSD 6AL what chip do you have in it. The MSD box could be shutting down and then relighting. You may want to just take the chip out all together.

Also, as mentioned above the condenser will also cause similar problems. As mentioned they are cheap and easy to replace. I have seen a condenser act like this in the past when the headers were changed.

What work if any have you recently performed on the car? This may give us some more clues.