Please try not to let your own, adult upset and embarrassment over your son's meltdown and departure color how you look at your daughter's experiences there. You need to step back from the emotions YOU feel, that are tied up in his problems while there, and be the objective adult when it comes to your daughter.
The fact you are "embarrassed and ashamed" and focus on the adults' "tight cliques" (that you're not part of) is not good. That's focus on you, not on your child.
When I read you post, many things I see you wondering about are things you could find out yourself or take in hand by being proactive:
You're not sure if she has friends. So ask her. Does she talk about other kids? Ask to see them outside school? (By age eight most girls, I think, are asking about play dates with other kids.) Does she talk about what Sally said or what Jane did in class today or how Jimmy is a joker? Have you ever talked with her teacher about whether she seems to be doing OK socially? Also, remember some kids are not social butterflies. If she has a couple of friends, and gets along well enough with the rest of the class, she's fine; she doesn't need lots of tight buddies. You also can help things along yourself, mom -- do you ever contact other parents to arrange play dates outside school? She can't do that herself.
Regarding the teacher: If she won't have the same teacher next year, I'd drop the concern for now about the teacher not being as communicative as you like. It will be different next year and you can tell the new teacher right up front at the start, "Do you enter a 0 when an assignment's not complete" etc. The portal you mention sounds a lot like what we have in middle school here -- we get e-mails from teachers with grade summaries and the summary shows if there is a missing assignment, and then we get an update summary that reflects the assignment when it's done. Surprised to see that at elementary level, but it's helpful. If the teacher is indeed updating as needed, why is this such a concern? Isn't it possible that it's just a new system for you so you're not confident in it because it's so different from what you're used to?
If you want a year-end conference with the teacher, why not contact her today to schedule it? Even if she does not do regular conferences for the end of the year, you have the right to see her. Are there at least one, preferably two, scheduled conferences each school year?
It sounds as if you're not sure whether this school is telling you the full truth about her progress. You say that her old school always told you she "was deficient in all areas of academics" then you say that "I'm not hearing that here" and have seen good grades -- but I get the feeling you are doubting something about the new school and maybe even about her grades.
Do you work with her at home; hear her reading out loud, ask her questions about what she's read; help her review for a history quiz to see if she "gets" the material; review her math homework to see if she grasps the concepts? If you are involved with her homework and with just talking to her about what she is learning, you will know if you feel she's getting a good education here and grasping what they are teaching her.
Overall your post sounds as if you are a bit scared to question the teacher or press to find out more about what she's doing IN school academically each day. If that's wrong, I'm sorry, but it comes across that you are so worried and ashamed over your son's short stay there that you are not being proactive or very involved with the school, the teachers and yes, other parents.
The fact your child, herself, is asking to stay there is VERY important. Ask her why she loves her school so much. Draw out some details by asking her specific questions: What is your favorite subject? Why? What is the most fun part of history? What does Mrs. X do when she teaches math that made it fun today? You might learn a whole lot about what seems to be working well for her.