Coming in new to ACKs but not D&D i found this quite an interesting read and something I've struggled with in the past. It is a tough thing to balance while keeping some simplicity and quick flow to combat.
For me mostly was the issue of HD being an indicator of mass and combat ability (accuracy).
Mass hp Vs Morale hp:
Like you found that large monsters had good accuracy (and high damage as they would), despite having obvious laboured attacks (ie slow and obvious to a trained combatant) or no training. The other side of the coin being smaller creatures with exceptional accuracy but low HD because of a lack of mass had low accuracy (like a snake for example).
In the end I just ended up winging it as to how much accuracy could be expected for a certain creature, used HD as a "level" (typically for spell effects and xp), and as a guideline as mass/fatigue.
At the end of the day for typical enemies hp as mass or hp as fatigue/morale didnt seem to matter all that much (for the overall combat), given players tended to dispatch them whatever the case. On the PC (and core NPC) side it mattered more, but as mentioned those hp tended to be more fatigue/morale in the players side of things.
What I have done previoulsy to represent that hp as mass for PCs (and enemies during combat), is adapted the Earthdawn notion of 'Wounds'. Essentially a wound is a representation of an enduring injury (ie physical damage) rather than the fatigue/morale that hp tend to represent.
Wounds were inflicted based on a good attack or high damage (in Earthdawn it is about a certain damage threshold, but damage is ever growing in earthdawn due to exploding dice, skill and raw strength) for the way I handled it. Essentially it was every 10 points (modified by con) of damage in a single hit (successful saves on spells prevented wounds, even if damage was taken), every attack roll exceeding the AC divided by 5 (rounding down), inflicted a wound (defeat the AC by 5-9 inflicts one wound, 10-14 was two wounds and so forth), or anytime 0 hp or fewer are reached gained a wound as well. Damage was otherwise still tracked by hit points as usual.
The results of these wounds was that any healing you recieved was reduced by the number of wounds you currently had, while every wound after the first one wound cause the character to suffer a -1 penality to all rolls per wound (ie if they had 3 wounds, all healing was reduced by 3 points, and they suffered -2 to all rolls). Often players made up the flavour as to what the individual wounds actually represented.
For greater mass creatures, I just let them take more additional wounds before penalities based on size breakdowns (large could take 2 wounds, huge 3 wounds and so on), while some creatures just never take wounds as well (like undead/oozes), others had special abilities to ignore more wounds (like constructs).
Healing wounds is a slow process. Character needed to have full hp first (by whatever means), then either a healing spell would cure a single wound (or more for higher level heals) or after sleeping a con test (vs 10 + 2 * <curent number of wounds> plus modifiers based on sleeping conditions or appropiate skills) to heal a single wound (a save vs death could be used for the con test in ACKs).
This could work with you wound concept that an orc has that 5 wound points, so will die if it has 5 wounds even if it still has hp left.
On Parring:
Warhammer fantasy has the parry rule in place but gives exceptionally strong or large creatures a special ability called Unstopable blows, it basically meant the creature was so large it gave significant penalites to the characters trying to parry it's attacks. This kind of thing can be added as a scalling penality based on size or even the creature itself, or even used as an "armour piercing" concept to reduce the benefirs of armour from those larger creatures it wounldn't help as much from.
We also liked the way Warhammer made shields a parrying device and not armour, so adapted it to a Castles and Crusades game in that a shield doesn't offer AC to melee attacks (still gave +1 AC to missile attacks), it instead lets a character using a shield gain a free parry once per round. This parry was an attack roll based on the kind of shield (bucklers (no bonus) and small shields (+1 bonus) used dex, larger shields (+1 bonus) used strength) with a DC equal to the attack roll, a success negated the attack. Likewise you could use a minor action (move type equivlent action) to take a parrying stance with any melee weapons, but still were limited to one per round (more than one quickly gets out of balance).
I hope these idea's give some more food for thought on the concept overall. :)