Wow, that is pretty acidic. I would worry about changing the PH too much in such a large ecosystem since you have so far to go to hit 7. Maybe shoot for 1-1.5 per season or something to let the pond settle out. Not to mention my tropical fish do very poorly if I change my PH more than 0.5 at a time, though admittedly it happens very fast in small aquarium.

At least if you add lime the alkalinity will increase as it combines with acidic compounds and then will buffer the PH a bit better around 7. Keeping that in mind due to low alkalinity it may not lake as much lime to get the pond in a reasonable state of PH. If it has survived this long at a really low PH, it will be fine raising it slowly.

Hmm, it would be interesting to toss in a load of my pulverized limestone clay from my pond. Would probably foam like crazy!