Ok, another wall of text about...
MONSTERS
All the Monsters files have now had at least one pass, which has involved little more than chopping roughly 50 or 60 creaures above CR12 (with a few exceptions). For the ones I did, I made some brief notes about what other probably ought to be cut; and how others might be modified. All those are just my personal judgment calls, of course, based on a quick look at each monster, so feel free to disagree with any of this! The following sblocks contain summaries:
Monsters that probably ought to be cut (25)[sblock]aboleth
basilisk, abyssal greater
greater barghest
demon, hezrou
devil, hamatula
devil, bone
devourer
formian myrmarch
genie, djinni
genie, efreeti
giant, elder stone
golem, clay
golem, stone
inevitables
leonal
kraken
night hag
guardian naga
ooze, black pudding elder
purple worm
rakshasa
roper
salamander, noble
swarm, hellwasp
wraith, dread wraith[/sblock]
Monsters that could probably be easily modified (39)[sblock]- acherai
- archons (subtype)
- blink dog (dimension door)
- various demons and devils (easy if gr.tport, charm monst, ether jaunt, trueseeing go into the "special abilities" glossary)
- derro (remove refs to confusion; and hi-lev cure magics)
- dryad (tree stride)
- earth elementals (remove ref to spell move earth)
- ethereal filcher, marauder (ethereal jaunt)
- genie generic (plane shift)
- genie, janni (ether jaunt)
- gibbering mouther ("gibbering" refs confusion in description)
- hag, sea hag ("evil eye" refs dispel evil in description)
- homunculus (construction refs arcane eye in description)
- invisible stalker (description refs trueseeing)
lammasu (spellcaster as Clr7; plus gr.invis, dim door)
- lamia (charm monster)
- lillend (hallucinatory terrain)
- lycanthropes (section "curing lycanthropy" refs heal, break ench in description)
- nymph (as caster Drd7; plus, dim door)
- minotaur ("natural cunning" refs maze in desc)
- mummy ("mummy rot" refs break ench in desc)
- naga--
--- dark (as caster Sor7=>not E6, but no spells over 3rd!)
--- spirit (as caster Sor7)
--- water (as caster Sor7)
- phantom fungus ("greater invis" refs gr invis in desc)
- phase spider (ethereal jaunt)
- satyr ("pipes" refs fear in desc)
- shield guardian (construction refs hi-lev spells)
- sphynx, androsphynx ("roar" refs fear in desc)
- sprite, grig ("fiddle" refs irresistibe dance in desc)
- sprite, pixie (gr invis, permanent image, irresistible dance; "memory loss" refs hi-lev spells as cures in desc)
- triton (summon nature's ally IV)
- unicorn (gr tport)
- vampire template ("dominate" refs dominate person )
- vampire spawn ("dominate" refs dominate person )
- vargouille ("poison" refs heal )
- will o' wisp ("immunity to magic" refs maze)
- xorn ("earth glide" refs move earth)[/sblock]
Monsters requiring more extensive/complex modifications (14)[sblock]- avoral
- barghest
- formian taskmaster (inline dominate monster text)
- ghost (telekinesis; "malevolence"refs magic jar in description)
- hag covey (6 of 8 SLAs based on hi-lev spells)
- half-celestial template (1of2 SLAs at 5HD are hi-lev; 1of2 SLAs at 7HD; all SLAs for 9+ HD)
- half-fiend template (hi-lev SLAs at 5HD and at 11+ HD)
nightmare/cauchemar (astral projection, etherealness)
- ogre mage (cone cold, polymorph)
- phasm ("alternate form" refs polymorph in desc)
- ravid (animate objects)
- sphynx, gynosphinx (legend lore, plus 7 symbol spells)
- spider eater (freedom of movement)
- treant ("animate trees" refs liveoak )
[/sblock]
Lastly, in the interest of simplifying potential mods, a handful of spells fairly frequently pop up as SLAs or Su's, and so might be good candidates to be rejiggered into "special abilites" and added to one of the "Special Abilities" glossary files.
Spells commonly used as special abilities:[sblock]ethereal jaunt
confusion
charm monster
greater invisibility
true seeing
dimension door
fear
greater teleport (which itself refers to teleport)[/sblock]
With all that said, there are now quite a few possibilties to finishing out the Monsters. First, I'm just going to assume that we'll agree on some version of the "probably ought to be cut" list and simply cut those monsters out.
The easiest thing to do is to simply chop
all of these monsters (or practically all of them), and forget making any other mods to the official SRD text. (I haven't actually counted, but I believe all these listed plus the ones above CR12 already cut accounts for around 25% of the monsters in the full SRD.)
Quite a few of them actually involve very little modification, and could be E6ified by deleting a single sentence, term, or subsection. For ex, shield guardian, iirc, could be fixed simply by removing its construction info. In the notes above, I tried to indicate nearly trivial mods like that with a pattern like:
"special ability" refs spellname.
Other mods are more involved, and generally fall into two categories:
1. A very few monsters are casters at 7th level or above, some of which get 4th level slots. Easy fix is give the monster a metamagic feat, and limit that 4th level slot(s) to a metamagicked spell. Another fix, also mentioned upthread, is to change those slots into SLAs. Either way, this is fairly straightforward.
2. The vast majority of mods, however, involve references to specific spells that doesn't exist in E6. An easy approach, as has been mentioned upthread, is to just make a list of "Monstrous Spells for Spell-like Abilities", and leave it at that. Another approach is to actually convert spells into special abilities somehow; this is potentially problematic (spell variables; spells referencing other spells; and so on), but we can discuss later. And if we go this route, I think adding the most common ones to one of the "Special Abilities" glossary files is wise (even if we end up in-lining all the info into statblocks for an online presentation later on).
Anyway, take a look at some of the monsters I've called out above, and try to get an idea of the magnitude of some of these sorts of changes. Frankly, I think that's easier than reading more of my blather.

Then we can decide exactly what to do a little later.
I'm looking forward to whatever input you've got!