Yes, allergies can definitely contribute since they create an inflammatory response in the body which compromises the effectiveness of the immune system. Allergies and food sensitivities very often go hand in hand with leaky gut.
There are many ways that you can contract parasites and doing a parasite cleanse 1-2 times a year is advised. Keep in mind that testing for parasites is not always reliable...it usually involves stool analysis and even if you have cleared your bowel of them they can exist in other areas of the body.
Not sure what you mean by 'lots' of B vitamins...B vitamins are important for a myriad of body functions, and some are produced in the intestines by beneficial bacteria. You could be reacting to something in the B formulation...vitamins are certainly not all created equally.