If we're going with Huge, I guess that would work. So you're suggesting base creature's AC with a +6 NA bonus for the wooden juggernaut? But each leg is made of 3 trees, and a treant is already Huge, so shouldn't these be Gargantuan with a correspondingly larger NA? This may be part of the issue we're having.
The rules for Juggernauts in
Jakandor - Island of War, which is basically the "Knorr sourcebook", says they are 30 feet tall. The illustrations on pages 5 and 70 of that book both show Juggernauts that scale to about 30 feet tall, assuming the human figures are, well, human size.
A 3E Treant is 30 feet tall, roughly man-shaped and composed of wood.
A standard Guardian Juggernaut is 30 feet tall, roughly man-shaped and composed of wood.
It seems reasonable to assume they are the same size category, which'll make the juggernauts Huge.
The flavour text description does talk about their legs being made from the "boles of three trees", but I guess they could just be very small trees! It also says its torso's "larger than an oxcart" which is less help than you'd think it would be, as it doesn't say how big this eponymous ox cart is.
It's worth noting that the illustrations on pages 4 and 141 of
Jakandor - Land of Legend show Juggernauts that look significantly bigger than 30 feet compared to the human figures in the picture. Maybe somewhere in the region of 50-60 feet? It's hard to tell. There's another picture on page 139 that show two battling goliaths who are several times taller than the
trees they stand behind. Unless they're very small trees, the constructs in the picture would have to be 100+ feet tall. I'm inclined to trust the "Knorr sourcebook" more on its scaling of these constructs.
In conclusion, I think it's easiest to say Juggernauts start out Huge sized, but if you want a bigger one it's a simple matter of using a base construct that's had its HD advanced to a larger size.
I can go with a Dex penalty and "cannot Run." Does that do enough?
The thing is, they're supposed to be used offensively, and if we give them that speed then ordinary humans on foot can use Run actions to simply dash around them.
Maybe we should just give the Stone variant the "cannot Run" trait, since the flavour text says they are mainly used defensively due to their lack of maneuverability?
It means we're dropping most the special maneuvering rules of the original rules, but frankly they'd be a pain to implement in game.