Some clogging questions

The exact location of the clog can depend on the instance. If you are using filament with poor diameter consistency, I suppose you could have it lodged before making it to the nozzle, but have never seen this...only clogs at the nozzle which then back up into the barrel.

If you are still using the stock PEEK hotend, disassemble it as much as possible with as little force as possible. Don't go all hulk on it. Once you get the brass removed, you can hit it with a torch and use something like a straightened coat hanger to plunge through the barrel. If using ABS, soak it in acetone for a couple hours. If PLA, acetone has almost zero effect on it, so you would need to use another solvent. One user on here used MEK for smoothing PLA parts, so you can try that.

A partial clog would cause irregular extrusion. One indication of this would be gaps in the walls of a print, though this could also be a couple other causes, not necessarily a clog.
You know you have a total clog when the extruder makes a clicking sound, strips the filament above the barrel, and refuses to extrude.

I have gotten a couple minor clogs and one major clog in my E3D hot end before.  In fairness, I put a lot of use on it and I frequently switch between filaments.

For a minor clog, I have just heated it a little hotter and pushed it thru until the clog breaks free.  For my major clog, I had to disassemble the nozzle/ heater block/ heat break assembly and soak the nozzle and heater break to break up the ABS.  I also somehow had a solid chuck of ABS melted inside the peek insert to about 1" up, which required the peek to be replaced.  I never found a cause and never did anything unusual to cause this so I just blame heavy use.  Still not a bad record considering that I put about 10 spools thru it at this point.

I have found that wrapping a rag around my filament (where it enters the enclosure)  to wipe away dust helps a lot.   
Any nozzle can be clogged with enough persistence

I think the rarest clogs are those from using too low a temp so extrusion is too difficult, since if that's all it was just raising the temp would cure them.  Some might be the filament (both shape and quality w/ fillers or colorants). 

Aside from a lot of crap in cheap filament, most clogs I believe ( maybe I'm wrong? ) can be caused by overheating your filament, producing combustion or oxidation type byproducts that accumulate or even softening and malforming the weaker hotend parts (in the PEEK original) prior to the nozzle itself and compromising the filament path itself.  Of course if one softens and moves the thermal sensor so your setting is further off the 'real' temp (than it already was, in the stock setup) and you compound the issue because you only know what the software tells you.  (Using an IR thermometer on a moving head is a pain and not very accurate, either.)

The E3D is pretty immune to killing itself (compromising the path) since it doesn't have any real nonmetal parts in the path, but could still be impacted by by-product accumulation until you go the full monty on it and complete the combustion like jago suggests (yikes! that would scare me to death to try).   I'm still on the stock hot-end and I've only ever had one clog early on with the black filament (I print all ABS) I originally got from SD back when they had some bad batches.  Others were successful just raising the temp and printing it but I didn't want to take the risk of causing further damage and binned it.  Stick to what I hope is good quality filament since, and do a fair amount (200-300mm) of test extrusion with any new color batch to decide on the minimum temp I think I can safely use.  I'm not that careful about keeping my filament dry so I do tend to get the little steam bubbles depending on the print conditions, but I don't think that would contribute to clogging.  Typically I set my hotend to 190-195C (knowing full well the real peak temp inside is higher, that's just what I tell the interface).  People who set the software to 205-210 scare me, but I guess with the E3D or other improved setups you both have a more accurate reading and way more margin than I do.

I'm also very religious about only heating the hot-end if I'm really immediately ready to extrude (e.g. if loading filament, it's already in the channel in the jigsaw just above the feed roller, bed is already up to temp and my finger is hovering over the mouse button waiting to click once I clear the cold-extrude limit) and powering it down to 85-90C (or off, if not planning another start) right after prints. 

And I use a very different filament route to make sure I'm not adding a lot of tension that's fighting the extrusion motor, either:  spools on hubs made with skate bearings, instead of the little hole in the back I route my filament over the top of the SD with a rocker-arm to both guide it and dampen the occasional fast movement pull so the spools don't start spinning and unfurl the whole mess on me, which is the consequence of too little hub friction.  My SD enclosure is basically tonsured like a monk ;-) . The goal of all that is to prevent (hopefully) tension which could starve the hot-end and increase burn product accumulation over time.  That's been my theory at least and I have no evidence to prove it wrong (why of course this elephant suppressant medallion is working...see any elephants in the room??). (Wonder if my guide/damper arm is also performing a little wiping action that's helping a bit as well? Wouldn't be the whole perimeter but certainly can't hurt...)

I  repeat, yikes!  I'm not sure my PSU would handle that, much less my PEEK-of-chit (I so funny!) hot end.