Hi jiminy,
If the new nail is growing out yellow it isn't because of the products you are using. But, that would be hard to say unless you completely stop using all products because it would just continue to stain the new growth making it appear that the new growth is coming in yellow. As far as Nail Envy, it is made by OPI and can be found in most full service salons that retail nail polishes.
Are you taking any medications or vitamin supplements in the last year or so? That could also be a cuplrit. I still think it is a reaction to the product you are using. If you had an infection, your would notice a change in the actual nail consistency by now. (like peeling, flaking, softness, crumbling, tenderness, etc)Also, infections usually don't show signs consistently on all of the nails at once, usually it starts on one finger and then gradually infects all of the nails.
You should use the strengthener as the base coat, then polish and then top coat. A separate base coat would defeat the purpose of the strengthener. A top coat isn't necessary if you don't apply polish. It sounds like you are applying the strengthener correctly. A far as remover, always use non acetone based remover, less harsh. I also recommend washing the residue of the remover off before applying polish. All nail products should be applied to clean, dry nails.
Did you try buffing one of the nails to see if the stain can be buffed off? That would also give you a clue as to whether or not it is the product being applied. If you can't buff it, I would have doctor look at the nails and see if there is anything systemic going on.
Let me know how it works out or if you have any more questions.
take care,
wendy