What we do is separate therapeutic activities (such as handwriting practice and fine/gross motor development activities) from academics, and use appropriate accommodations and modifications for academic work as needed to ensure that the work accurately reflects ability and effort, not disabilities.
For your dysgraphic and dyslexic daughter, for example, it really sounds like a scribe and/or permitting oral responses in place of written responses would be appropriate classroom accommodations for written work other than specific, targeted OT-directed handwriting instruction, until she can become independent with keyboarding or speech-to-text software. BTW, in-school instruction for keyboarding or use of speech-to-text software should be included in the IEP: it is surprisingly common for schools to provide Assistive Technology to kids but then not teach them how to really use it effectively.
For activities like the fruit loop stringing, the counting should be separated out from the motor component - once she's counted out ten piles of ten fruit loops (often a motor challenge in itself), then she can string them, rather than trying to keep track of counting and stringing together.
Her teachers should be instructed to clearly define the academic objective of each class activity and assignment (something that they should be doing anyway), and provide equal opportunity for her to access the curriculum and demonstrate mastery of those objectives in ways that are not impeded by her disabilities.
