A couple thoughts from a parent who is further along this journey (dd is 12 and an 8th grader):

Some of the things you mention sound a lot like my dd at that age. Particularly the following:
Originally Posted by amazedmom
...LOVES science and has asked for a 3rd grade science textbook after looking online at the quizes that went with it and being able to answer most of them correctly even though she has never been exposed to most of those concepts. She wants to be an orthopedic surgeon and "fix knees" and an "astronomer and study cool things in space, like astroids, and comets, and dwarf planets) Although she asked me the other day how she could do both.
My dd has been seriously focused on marine mammology with a specialty in sirenians since age three. This is still what she wants to do.
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I was told by her last Pediatrician to prepare for college at an age when she should be in middle school and in LOG she fits somewhere between a 4 and a 5. She hit every 4 milestone well before the ages listed, and in the descriptions, fit those about a year before they were done, but is slightly behind the level 5 milestones.
While our ped never said anything of that sort to us, dd12 fits squarely into Ruff's level 4. She is not PG, though, so you may be in for a different route. All I can say is not to think too far ahead. Just plan for what she needs right now. My dd started K on the young end (early fall bd) and skipped 5th grade. She is still a stellar student and tests in the 99th percentile of everything except math post skip (same place she was pre-skip), but I don't believe that she'll be accelerating any further. Due to her slower processing speed and general happiness with where she is now, we feel that she doesn't need further acceleration.
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She gets extreamly overwhelmed with crowds. ... She says the noises hurt. She also says this about my blender, or beaters, or the electric can opener and food processor, and the vacumme. So I am not sure what is going on with that. Any ideas?
We had the same with dd. She has sensory issues (overresponsive to noise and light) and is an introvert. She was dx with SPD/SID at 7.5, but has learned to cope as she's gotten older and, honestly, I believe that I could have been dx with the same as a child had anyone wanted to do so. It isn't debilitating for dd as an older child although it did lead to her never sleeping as a baby/toddler and being really high needs.

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I also dont see them getting as "locked in" as Dh and I call it. She gets very locked in on what she is doing and is extreamly quick to anger, like snap your fingers quick, and is in a full blown temper and anger if she is forced to stop. She seems physically distressed if she is not able to complete what she is doing in the exact perfect order. She also quickly angers if the person playing with her did not understand what she wanted and does it wrong or if "acting out characters" as DD calls it, is not done exactly the way she envisiond. Is that normal for 3.9?
We sort of had this, sort of not. Dd had huge, melt down temper tantrums until about age 5. She morphed into a lovely child at 5. I didn't see her getting locked into something she was doing, but the temper tantrums were definitely there. I had neighbors who thought I was abusing her b/c she screamed so loud and so long. It took two adults to get her into a car seat if she was melting down as she arched her back and shrieked.

The things you mention that I did not see in my dd would be:

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She also can not be still. She can focus, very well if it is something she is into....but she is CONSTANTLY flapping and wiggling her fingers. Not her hands, just her fingers....ALL DAY. ...
She also has a difficult time making eye contact. She will be listening to me or talking to me, but her eyes will be looking across the room in the other direction. When I tell her to look at me and I am talking to her, she will face me, but her eyes will be pointing in the other direction.

In any case, I'd see some of what you mention as possibly normal for an intense HG+ child, some of it possibly indicating sensory issues, and the lack of eye contact and flapping as something I might investigate more as possibly indicative of an ASD.