Nothing really. I just can't be in close quarters with tons of people for long periods of time.
I can wait on lines for as long as possible for rides like Peter pan, winnie the pooh, TTA, Speedway and it's a small world, because they have an "opening" for the air to circulate. I can't not wait in lines like spaceship earth, pirates, buzz or any rides that are "closed in".
When I take my mother she gets the GSC and just as the line starts to go up into the building at SM she would go around the back. When we would go on TSMM just as the line got to the "closer" quarter section we went through a different way.
I don't want to just "cut" the line as some people might assume. I know some lines can be up to 2 hours in close quarters. I just want to be able to enjoy my trip with my kid(s), and not have my kid(s) doing everything by himself while I'm waiting outside all the time.
I already can't go into the character lines like the meet & greet place in Epcot, the Toy Story friends in HS and probably not even Main Street theater in MK. I can't go into LM, GMR etc. so I thought if I can cut down on some wait times we would be able at least somethings together.
I don't understand why you can't go to many of these areas. My autistic daughter never could wait for 40 minutes for an attraction but that's why I plan like crazy so that we won't ever be around these kinds of waits. A good touring plan is worth
my weight in gold (and I'm no skinny minnie).
At Buzz, I've never waited more than 5 minutes to board using a touring plan and FPs.
At Pirates, my plan has us getting there when it's walk on or practically walk on. I've never waited more than 10 minutes.
The Toy Story M&G at DHS you can get in and out much faster than 40 minutes if you head there right after riding TSMM in the morning. Another option is to watch for your child getting up to Buzz through the window. Of course you can meet the same characters at MK outdoors so it's probably not worth dealing with it at DHS.
If you go to the Character Spot at Epcot at RD while somebody runs over to to the Land to grab Soarin' FPs then you'll be in and out of CS pretty quickly (10-15 minutes max if you're there waiting at the turnstiles well before RD, possibly even less depending on just how early you get there).
The princesses and Mickey have FPs at MK now meaning you can be in and out in 15-20 minutes (princesses take a bit longer because you see 3 of them).
Frankly, I'm really not understanding how the bolded works. I'm not aware of a back way in and how is anybody even notified when it's time to bring her in? Using FPs should mean no more than 25 minutes max (usually less) from when you first enter the queue until you're back out of the building, probably less. Why wouldn't this work for you? If you're at the park for RD and bee-line to TSMM then you'll be out even faster. If there are other concerns that you haven't mentioned then obviously this wouldn't work but with what you said I don't understand why it wouldn't.
I really think you should take another look at touring plan services. You'll be amazed at just how quickly you can be in and out of attractions. It will also help you to plan for alternating outdoor with indoor attractions to help kind of air yourself out.
There will still be some attractions that just likely won't work because of the waiting area (VotLM, Laugh Floor, any show with the pre-loading waiting room really) and I can definitely sympathize because many don't work for my DD either for the most part meaning we don't go to them either but attractions that don't put you in a room to wait really are totally doable within your timeframes with a good touring plan and FPs.
What is the difference if I wait 30 minutes in the assisant line at Spaceship Earth or 30 minutes in the regular line? I'm still waiting 30 minutes, but not with people crowded on top of me.
The alternate waiting area for SE is indoors. The regular line is mostly outdoors and only takes a few minutes once you get indoors. Why would you want to wait in the alternate area? That would be the exact opposite of what you said you need. That's one ride actually that I wouldn't recommend for somebody like you just because there are several areas with artificial scents piped into the ride and I would worry that it could send you to the hospital just from being in the ride.
So you would suggest taking advice from someone with a latex (touch and airborne) and over 10 other known airborne allergies (not including the food ones) who lives in the parks? 
I would think taking something every day would lessen the chance of a reaction and then if something did become severe, you could pop a benedryl. 
