I am running your same Pioneer sub 3002d4 off of an Orion 2500d amp. I have it wired down for 2 ohms, which pushes the amp to 1700 watts RMS, according to the manual. My sub pounds. Granted, probably not comparable to any sort of competition level sub, but I agree with everyone here that there has to be a severely clipped signal at the root of this problem. In any case, I'm pushing my sub, at least on paper, harder than you are pushing yours and it delivers (for now). Therefore, there is no need for you to reduce the power of your amp.
RMS v. Max wattage: RMS wattage is the typical output wattage of your amp, this is in no way the most it is ever going to put out. That's where "maximum wattage" comes into play. Although you can rarely trust manufacturers ratings for wattage, especially max wattage, it is possible and likely that for short musical bursts, your amp will push its max wattage. Think of it operating as a sort of "wattage capacitor" It stores and is capable of (in a quality amp) pushing that maximum wattage for a verrry short burst in the music. Of course once it does, it now draws more electrical current from your system to recover, and if your alt/wiring isn't up to the task, you get even more clipping.
What is stopping you from getting an aftermarket head-unit with RCA preouts? I agree with everyone here that a clipped signal from that head unit's amp will severely screw you up. Also, if it's like most stock head units, it's trashed after a few years.
