Lemme start by saying I don't know what hit the Pentagon. I would like to know, but I doubt I ever will, with any certainty. It could very well
have been a plane, or a missle, or some hybrid one-off creation resembling the former that functioned as the latter.
I just don't know.
That said, I'll address what I think are some logical errors you've made.
No allegations have been made of anyone seeing an airborne vehicle (helicopter or jet) firinig any sort of missile that day, and if one did there
would have to be some account or testimony.

There's a fair bit of farmland in the vicinity, as well as a (very) large body of water, and a handful of large-ish national parks. Just because
nobody saw a missle being launched, doesn't necessarily mean that it didn't happen. I don't always see my mail man coming, but I know he's been
there when I see the mail he's left.
Ground fired missiles are usually fired at air targets, it is unlikely that someone on the ground fired a missile into the pentagon, and there is no
evidence to support this claim. The only possible alternative I can see as remotley feasible is a long range missile.

The only plausible missle theory I've read involves an air-launched cruise missle variant.
A low-altitude missile could not have possibly worked because the pentagon is surrounded by buildings as it is right across the river from D.C, the
missile could not have stayed parallel to the ground and hit the pentagon without first hitting buildings or trees or whatnot.

Just because a missle has the capability to fly at very low altitudes doesn't mean it does so at all times, or has to do so. The way I understand
it, ground-hugging cruise missles approach the target at high altitude, until they get close enough to have to worry about AA fire, then they drop
down and hug the landscape to avoid SAMs and AA guns. If there's a tree in the way, they pop up, fly over the obstacle, and sink back down to
continue the approach.
Like you, I'm no expert, this is just what I've picked up along the way. A missle that can vary its approach and altitude, and does not rely on a
pre-programed angle of attack is more survivable because it's less predictable.
This picture is OLD (The Battle of Normandy), but it serves to illustrate a point.
Why fly through that when you can fly under it? Modern cruise missiles have to contend with even more AA threats, and to counter the efficacy of
radar and AA installations, some of them hug the ground to the greatest extent possible.
The video that aired immediatly after 911 showed the object hitting the pentagon appear to be almost parallel to the ground. Missiles do not work like
that.

Now you're making a broad and unsupported generalization. Missiles come in all shapes and sizes, and they behave in a number of different ways,
limited only by their software, hardware, guidance systems, and the ingenuity of their controllers in the case of fly-by-wire or otherwise
remotely-controlled examples.
It would have hit the pentagon at more of an angle, it could not have possibly been parallel to the ground because if it were at such a low altitutde
it would have struck other objects first before hitting the pentagon. The missile would have most likely impacted the top of the pentagon, not the
side.

The missile doesn't have to choose whether it hugs the ground or flies high and comes in at a sharp angle. It can adjust altitude to avoid
obstacles, while remaining as low as the terrain will allow to defeat detection and countermeasures.
Missiles do not leave impact holes. Why? Well, when a missile penetrates its target it then explodes. As seen in the video it basically blows
everything to #. My point: The hole created by the penetration would not be there because it would have been blown up with the explosion. A missile
would have left an impact crater, not a small hole. Most of, if not the entire wall would have been gone, there would not have been a small hole in
it!

That would depend entirely upon the warhead. Some missiles are designed to penetrate to a desired depth before exploding. Other missiles are
designed to explode on impact or explode prior to impact, depending on the objective and how hard it is. Make no mistake, the Pentagon is a HARD
target.
Look at the way anti-tank rounds work. They strike the armor, creating a massive amount of friction, and the charge is not so much an explosion as it
is a super-heated column of molten metal which bores through the target and kills everything inside.
Shaped charges direct the blast pressure and the resulting heat to magnify the effects. Here is an image of a shaped charge detonating underwater.
See the shape? This is the principle behind armor-defeating munitions - they don't explode in a big, uncontrolled bang. They burrow through hard
targets using the enormous heat and pressure created when a big explosion is focused into a small area of effect.
Missiles usually leave buildings looking like this
ptaff.ca...

Apples and oranges, as I've said - different munitions produce different effects.
The diameter of the whole in the pentagon was 2 and 1/2 yards. Despite the fact that a missile would not have left such a hole, even if you still are
not convinced then find me a missile who's diamter is 2 and 1/2 yards. Most missiles are barley a meterin diamter, no where near 2 and 1/2 yards.

The diameter of the missle is not necessarily equivalent to the diameter of the 'entry wound' - if the missle was designed to essentially transform
itself into a spear of fiery metal upon impact. If that's the case then the hardened penetrator at the tip might immediately plow through the
concrete, leaving a small hole - but now the mass of super-heated material travelling behind it is trying to fit itself through a very small space.
It will obviously widen the hole as it passes through.
So, you see, the missile doesn't have to be 2 1/2 metres to leave that size hole.
If I'm not mistaken, the successive holes were smaller and smaller, as if the penetrator kept going, but the charge following behind sputtered
out.
I have suspected for some time that it was not a vanilla passenger aircraft, but I was reading something the other day about depleted Uranium used as
ballast in the nose of airliners, so that's food for thought. Don't know how accurate that is, but it was something I had never considered
before.
Anyway, I'm not interested in convincing you, or anyone else, that it was a missile. I don't know it was a missile.
I can't very well convince someone of something I don't even know myself.
I just have a keen interest in uncovering more information about what happened that day, and analyzing it to the best of my ability.
So, please don't take my post as an attack. I appreciate threads like yours, that present evidence (wrong or right) and don't simply seek to attack
the opposition. I'd rather be shown why I'm wrong than be told I'm an idiot for being wrong, yaknow?
So, kudos for going about it the right way.