Ratdog is right. Some aftermarket stuff is better than others. Most of the time using Genuine HD stuff you wont have fitment issues with stuff, depends on what mods you are stacking together though. As far as relocation kits, Anytime you mod one thing it affects other things, doesnt matter if its an undertaill on a Honda or Sissy bar etc on a Harley. There are so many aftermarket parts available for HD with so many possible combinations its almost impossible for parts designers to make everything interact perfectly.
As far as reliability, anyone that thinks a HD from the factory isnt as reliable as any other make is stuck in the 70's or at the best the early 80's. Even highly modded HD's are easily very reliable with today's technologies. My FXR is pushing twice the HP it came with stock( and much more than a new HD), in an 18 yr old chassis and has had zero issues since I put it together almost 2 years ago, over 12,000+ miles. Shoot the stock evo in it was still running fine in 2007 when I pulled it, I just wanted way more power.
"He was a wise man who invented Beer"--Plato