Ok, so are we getting rid of the poison and then going with a disease that does Str or Dex damage and lingering pain (-1 penalty)? I'm not quite clear on what we're doing.
Ok, like this?
Agonizing Venom: DC X Fortitude negates, initial damage wracking pains (imposing a -4 penalty on attack rolls, skill checks and ability checks) for X minutes, secondary damage pain inducing a -2 penalty as above for X hours and pain inducing a -1 penalty as above for X days subsequently. The save DC is Constitution-based.
So you get some wracking pain if you fail the second save? I guess that works. Sure.
I think the climb speed is ok, but I'd drop tremorsense. I'd also probably decrease the swam damage a little. Centipedes and locusts do 2d6 and are considerably higher in HD, and these seemed kind of weak in terms of damage anyway. 1d4 plus poison?
Added to Homebrews.
Let's just call it "poison", since it essentially is just that. Otherwise, we'll have to add text indicating that it is treated as poison for purposes of immunities, spells, and so forth.
I used the spider swarm as the basis as suggested upthread. Should we retain the climb speed? What about the tremorsense?