Approximately how many grams of protein are you getting a day? Are you eating enough solid food or is everything mush? I cook all my food at home but you can still cook unhealthy food, e.g. I deep fry a lot. I personally couldn't get enough protein from just tofu. My normal breakfast and lunches both have a serving of seitan, and I eat a block of tofu for most dinners.

Your problems may stem from things you've added to your diet rather than things you've subtracted. E.g. if you replaced meat with beans but beans are making you shit, the solution is to replace beans but not necessarily to replace beans with meat. If you don't already have one, get a bidet while you're trying to get firmer poops. Ultimately, if you're concerned your body is decaying the way to check is to get tested.

Note that your B12 supplements may not be enough! I've been taking 2500mcg once a week and my blood level is still 333pg/ml which is low. I'm going to increase that to 3x a week or so and retest in a few months. Going vegetarian is already more work than blood tests, so I strongly encourage you to get some "objective" idea of what's going wrong and make other dietary changes 1 at a time if the tests are fine.