i just finished running a fairly successful game that ran for about 15 months. regular play, 4 PCs with the occasional guest player, 2-3 hours about every two weeks.
this is a long time gaming group, and it was my turn to GM. we are kind of burnt out on trying to learn new game systems (burning wheel, heroquest, savage worlds, etc.) but everyone is quite familiar with dnd 3.5, and a couple of the players also participate in a high-level pathfinder game, so we used 3.5 E6 with some pathfinder mods and houserules thrown in. the E6 aspects didn't really come into play much, as the PCs only recently progressed to 6th level.
i ran Tyana's Shade, 100 Bushels of Rye, Field of Daisies, a bunch of the scenarios from the 3 Harn Pottage collections, and other stuff i'd composed myself.
you asked about how PF E6 might work:
for the most part it worked well for us, probably because of our familiarity with the d20 system. dnd has some fundamental flaws and a few of the rules are quite FUBAR, but it's been around long enough and has been refined enough that there will be at least some kind of rule system to guide you in resolving whatever comes up.
my main beef with 3.5/PF is that it is level-based, with a power curve that quickly gets ridiculous. i though the E6 limit would mitigate this, and it did, but not quite enough. many harn scenarios work great for PC levels of up to about 3rd or even 4th, but at some point, to keep challenging the party, it becomes necessary to beef up the opposition. sometimes this starts to push the bounds of the realistic low-fantasy harn environment that i like so much. but if you like a more high fantasy game, this won't be a problem.
i did keep the amount of magic items quite low. the players didn't seem to like that at first, but once they figured out that the bad guys didn't have them either, things were fine.
one thing that was really cool was how the wizard reacted to harn's societal views on magic; he spent a lot of time worrying about being burned as a witch, hiding his spellcasting, etc. as a result, he had to be much more clever and creative with less flashy magic. but this was more of an environment/role-play thing than a rules system effect.
if i had it to do again:
severely curtail magical healing! this is one of the biggest problems with PCs - one spellcaster with healing magic means that the players have easy, instant, and essentially free replenishment of hit points. my preferred vision of harn is that healing magic is NOT commonly available, so my NPCs seldom have access to it. this is a problem with both balancing encounters and with suspension of disbelief (for me, anyway). i had more that one battle where some PCs absorbed more than twice their total hp and still lived. hey, sir coagulate - let's see how brave you are without that damned cleric standing behind you!
i tried to group the 3.5 spells into pvaric schools, which didn't work out so well. probably better to just have the shek-pvar use the 3.5 "schools of magic" (enchantment, evocation, necromancy, etc) instead.
i might try the d20 variant rules "defense bonus", "armor as damage reduction", and "vitality and wound points".