questions/issues/bugs:

-"You can't build while in the air." -- what is the purpose of this?  if it's to stop pillars, you can still basically make them by building 2 pillars next to each other and jumping back and forth.  also, it seems to consider you in the air if you're crouched and on a ledge.  i'm not sure if you're trying to prevent building over gaps with that?  one possible downside: if you fall in a hole, you might not be able to get out of it.
-the swimming while encumbered thing.  is that just supposed to make swimming annoying but you can still kind of get free if you're persistent, or is it supposed to hold you fast?  are you just supposed to sink down and walk on the bottom (it seemed we could)?
-i unpacked the .jar file to a folder (ExtraHardMode31a2) so i could see the permissions in plugin.yml, and on the next boot got this in the console: "05:15:43 [INFO] While loading ExtraHardMode (plugins\ExtraHardMode31a2.jar) found old-data folder: plugins\ExtraHardMode31a2 next to the new one: plugins\ExtraHardMode"
-is it intended that ghast fireballs can destroy cobblestone?  maybe add a toggle in the config if so.
-having ghasts impervious to arrows AND giving potion effects when being hit by their fireball felt excessive.  there's a config option for arrows but not for potion effects.  actually, if we could have a percentage chance of being affected by a potion effect for each mob type that has one, that would be nice, and you could just set it to 0 to disable it.
-a user said he saw some blocks he was approaching in our cave just disappear.  i didn't see it and he didn't sound 100% sure but FYI in case you hear it again.
-it seems if you hit a zombie when he's in a cobweb, the web disappears (and possibly nearby webs also).  that might be intended though to make them more deadly?
-a user said he was lagging during the rain but all of our torches were inside in our cave.  i toggled the weather on/off a few times and it seemed consistent for him (no lag with the rain off/lag with it on).  i didn't have the lag but i'm also playing on the same network as the server and my pc is a good bit more powerful than his.  perhaps that routine may cause lag still for certain people or in certain situations.  we only had maybe 20ish torches in the cave near us.
-we were able to create an infinite pool (4x4) of water using 2 buckets and very quicly placing them in opposite corners.  i'm not sure if you're trying to prevent this based on 'buckets will not move water sources' but if so, FYI.  this is also doable with 2 people if you're not quick enough alone.  having the 4x4 infinite pool then lets you easily expand it to a bigger pool.
-irrigating is non-trivial - we were able to put water from a bucket into a 1x1 hole that was pre-surrounded with soil and then plant seeds on it.  the soil seemed to hydrate after that and the crops grew ok (though some died).  i'm not sure if that's intended.
-when mining coal with a stone pick, it softens the stone around it, but when mining a stone block with an iron pick, nothing is softened.  is this intended?  it almost seems like the whole cave/cave-in mechanic gets a lot easier once you hit iron.  maybe the bracing/support system mentioned below would be needed if this is changed though.
-dbo web page says: "The TNT recipe produces 3 TNT" - is that technically 4 with the default config setting of "More Tnt Per Recipe: 3", so the 1 you made + the 3 extra?
-from the config: "Arid Infertile Desserts: true" - desserts are food, but the though of them being arid and infertile if overcooked was amusing :)
-dyed sheep turn to white if they eat while dyed.  the description of this feature makes it sound like they shouldn't change until you shear them one time but maybe you are just supposed to be quick?
-"Plants need natural light to grow. Plants which don't get sufficient natural light will die." - i bonemeal'd an underground seed that was lit by torches and it grew to full.  we also had wheat growing underground without bonemealing it at all.
-potion effects aren't respecting "god mode" (essentials/worldguard).
-silverfish "Cant enter blocks: true" - is that only for skeleton-shot silverfish?  we think we saw some natural ones disappearing.
-is it intended that you can use the falling block mechanic to safely put out fires in the nether?  you have to place them high enough so that there's 1 block of air between the fire and the block that is placed (that then falls on it).

new ideas/enhancements:

-option to 'catch a cold' if you stay out in the rain too long, maybe mitigated by armor
-use fences (or some other configurable block) as supports, which would protect a certain radius above/around them from softening/caving in.
-configurable encumbrance, either so you can specify what items weigh and/or allow us to increase/decrease the overall amount of weight you can carry before encumbered.
-an option for a chance to collpase what's under you if it's 1 height and you walk on it?
-use long grass instead of dead bush for wheat death?  i guess that depends on your tpack but a user thought it would look closer.
-it seems like iron pickaxe breaks really quick when mining stone (we were able to break 28 stone blocks before it broke, and about 68 for a diamond pick).  i think that's intended but maybe we can get a multiplier for each type (iron/diamond) so we can get it exactly how we want, and maybe also a multiplier for the other tools and weapon durabilities too.
-list the permissions on the dbo page or add a link for the full list.
-maybe stop spiders from dropping string normally since they're already dropping tons of webs and that's seriously a lot of string.
-"Extinguishing Fires Ignites Player: true" - maybe have a percentage like with breaking netherrack.  having both was really annoying my one player.