I've worked with agar a lot, and made a few things from the HRC. Of all of the things you've identified as possible problems, I think the biggest likely ones are the quantity of agar, and the agar powder itself. Everything else about the cooling issue is normal. Agar powders do vary. You want to find one that is pure, unadulterated agar, not one that is setup to be a pre-prepared dessert as those are weaker.
If just for a laugh you want to try to save this batch, heat it back up until the agar fully melts, shear in a second amount equal to what you did last night, making sure it fully dissolves, then let it set again. I'm pretty sure that will work.
You can also pick up a sub-gram scale on Amazon for around $20. Thanks, drug dealers! They are very helpful when making small batches of "molecular" recipes.
This depends on what you mean by a gelatin "substitute".
What you have to understand is that while most hydrocolloids have gelling and stabilizing properties, they are not simply interchangeable. You can't substitute one of them 1-for-1 where you need gelatin and expect everything to just work.
A great place to start would be the Hydrocolloid Recipe Collection which, despite its name, is almost more of a cookbook, because it has detailed information on the properties of each hydrocolloid.
Agar is actually a stronger gelling agent than gelatin in the sense of having to use less of it to get the same strength, but you need to use it properly. The most important property of agar is that unlike gelatin, which gives hydration at temperatures as low as 50° C, agar requires a temperature of 90° C. In other words, you need to heat the water all the way to a rapid boil before the agar will actually "activate". A light simmer is not enough.
The other notable property of agar is syneresis, which is the loss of moisture over time. Agar sets extremely fast compared to gelatin and above room temperature, but unless you combine it with a small amount of Locust bean gum, it will actually dry out. Otherwise, though, you can absolutely, definitely substitute agar-agar for gelatin if you actually get pure agar (I made the mistake of buying the "dessert agar" once, which is not the same thing) and hydrate/set it properly. In fact, the biggest concern with using agar as a substitute for gelatin is that you might end up with something too stiff, since gelatin produces a much softer gel.
Perhaps the closest hydrocolloid to gelatin in terms of its properties is iota type carrageenan. Here's a side-by-side comparison of the most important characteristics (this is all taken from the HRC):
Property | Gelatin | Carrageenan | Agar
------------------+-----------+-------------+---------
Thermoreversible | Yes | Yes | Yes
Strength | Soft | Soft | Hard
Elasticity | Elastic | Elastic | Brittle
Shear Thinning | No | Yes | No
Hydration | 50° C | 70° C | 90° C
Setting Temp. | 15° C | 40-70° C | 35-45° C
Setting Speed | Slow | Fast | Fast
Melting Temp. | 25-40° C | 45-80° C* | 80-90° C
Viscosity | Low | Medium | Low
Gelling Conc. | 0.6-1.7% | 1.0-1.5% | 0.2%
Syneresis | No | No | Yes
You should be able to see by this how much closer carrageenan is to gelatin; trouble is, it's difficult to find, and you have to get the right kind (the kappa type and other types have very different properties).
There's actually an even better type of carrageenan to use a gelatin substitute, if you can find it: It's called Ceambloom 3240 and it's specifically designed to be a gelatin replacement.
I'd like to also note for the record that the answer in your ochef link is not really appropriate for gelatin desserts that need to hold their shape. Xanthan gum is a fantastic and versatile hydrocolloid but (to the best of my knowledge) it does not "set" the way that gelatin, agar, or carrageenan do. It's more of a thickener/emulsifier/stabilizer, at its highest concentrations being used to produce foams (but not gels). It's often used to stabilize other gels/foams but I've never heard of it being used to create a gel on its own.
Guar gum is also largely just a thickener, that you could use a stabler replacement for corn starch or arrowroot, which is also mentioned in that answer. None of these are appropriate at all for gels (desserts), they are only useful as thickeners.
Best Answer
The difference between activating them is important if you want to use gelatin instead of agar. Gelatin is made of proteins and peptides and agar is a polysaccharide.
Gelatin should not be boiled, because it breaks down. Agar needs 95 deg C to dissolve, so usually it is simply boiled. This means, that if your receipe calls for boiling the agar with stuff you want to gel (e.g. fruit), you have to add gelatin later, when all the boiling is finished, but the mixture is still hot enough to dissolve the gelatin.
Also, agar will work on some fruit, that prevent gelatin from geling, like pineapple or kiwi. If you want to use these fruit with gelatin, you have to boil them (or so they say - I have access to agar, so I never tried gelling boiled pineapple with gelatin).
Oh, and about the proportions: 1% agar as stiff as a jelly bear, 0,5% agar is as stiff as a normal jelly. One teaspoon agar weighs 3g, so it will make about 600ml of a jelly.