Great questions and great catch in terms of getting out that large Rope. Our youngest son had basically the same symptoms early years on. He also had the same acne, until we he cut way back on wheat; it was mentioned at the Andreas Kalcker conference the possible connection with gmo's and grain, which you may already be familiar with.
Personally I feel there is a connection between the gmo's introduced in the 90's...because our son who was on formula (first ingredient corn syrup solids????) had most of the symptoms that have been expressed in relationship to the Rope Worm/living fungus. I do feel many children are born with this "living fungus/parasite" already getting started.
If you get a chance can you please upload your picture to the CZ parasites image page titled "Ropeworm."
Someone also mentioned at some time that the gel stage creates a bad reaction to immunizations?? Forget where that was mentioned, perhaps the CD Autism site.
Personally I would just focus on getting this stuff out while your working on whatever your Dr. thinks is important.
Of course your immune system is out of whack, it's doing it's job trying to get rid of this stuff for you, but it's attacking all the wrong things because it can't. I've been there and I feel for you. You may want to try the 4 day alternating diet to give your immune system a rest; only eat whatever your sensitive to one day then take 3 days off so your immune system doesn't create antibodies to it.
Also since Ropes have a fungus element I found that most foods and vitamins that I had a reaction to most likely had trace amounts of mold (this fungus seems to not like mold)
therefore I froze my vitamins for a couple of days or took a wee bit of Vit C powder ( Hulda Clark ) with whatever foods I thought may have trace amounts of mold to kill mold spores which stopped the reaction.
Sending healing thoughts and strength your way