Just a thought... If the big bump on the side/base of your big toe is hurting, reddish and seems a bit larger, it could be a bunion. Suwariwaza will not cause a bunion but will surely aggravate it if you are starting to develop one anyhow.
Bunion is an enlargement and deformity of that joint/the bones on either side of it. Worth seeing a doc to check on it. Wearing shoes that are super wide up front to relieve pressure is really important. Not doing suwariwaza during a flare up (you can't cure them but they do wax and wane in terms of aggravation) is IMHO very important too.
If you do not have a bunion, you still might want to reconsider doing suwariwaza. Its one thing to sometimes have aches and pains. Its another to develop a pain that happens each time you do something. Your toes are sending you a message (and, with a torn acl--brace notwithstanding--you are at high risk to be damaging your meniscus and developing osteoarthritis with the amount of pressure on your knee joint....but that's anther story...)