CS #27 -- Other: This appears to be a parenthetical interjection to the effect that her brother is a turkey. I must admit, I would leave to my editor (if I had one) to punctuate it: "She makes a great big turkey -- I wish it was my brother, and she alway's allway's makes a gigantic pot of fudge." or "She makes a great big turkey (I wish it was my brother), and she alway's allway's makes a gigantic pot of fudge."

RO #40 -- Other (probably careless): A pronoun reference problem may have been pitting stress on STM. Note that the "them" appears to refer to the dead puppies and gerbils, but it was meant to refer all the way back to grandparents.
RO #41 -- Contrast (or subordination) The writer may have had in mind the contrast between work and play: "I clean house for about two hours; then I go out and ride the motorcycle, mopad . . . ." Subordination of the second clause would lose the contrast, replacing it with a purely temporal connection: "I clean house for about two hours, after which  I go out and ride the motorcycle, mopad . . . ." 
RO #42 -- Subordination (or amplification):  Subordination works here, but so would amplificaiton: " . . . then I go out and ride the motorcycle, mopad, which is a lot of fun." or " . . . then I go out and ride the motorcycle, mopad, because it's a lot of fun." or " . . . then I go out and ride the motorcycle, mopad -- it's a lot of fun." I'm wondering if part of the problem here is that "which" tends to modify just the "motorcycle, mopad," whereas the fun is in the going out and riding? The main point, however, is that here the student had three possible options, each of which slightly affects the meaning. Most instruction in grammar does not relate it to meaning, and so this student, at a loss as to how to handle it, simply left out the punctuation altogether.
RO #43 -- Amplification (possibly subordination): It is possible to eliminate the run-on by using "because": "At Christmas it's the most fun though, because we get a lot of big expinsive fifts and a lot of money." This turns the second clause into the reason for its being fun, rather than a part of the fun: " {At Christmas it's the most fun though -- we get a lot of big expinsive fifts and a lot of money. She makes a great big turkey, . . ." I'm suggesting that the student could have used "because" if that was what she meant. The run-on probably results from her not knowing how to use the dash to express amplification.
RO #44 -- Other (possibly subordination):  The student wrote: "I usually stay with her a couple weekes after Christmas to clean up \R\ we alway's have big get togethers around the holiday's" I suspect a cause/effect relationship was in the writer's mind here, but the sentences did not come out right: "Because our get-togethers around the holidays are always so big, I usually stay with her a couple weeks after Christmas to clean up."
RO #45 -- Other (probably careless)