Your dd's challenges with reading and spelling sound very much like my dd7 who is in 2nd grade. I think there may very well be literally 100s of different reasons that this type of thing happens, but fwiw, this is what we've just found out re our dd (she has recently completed an educational eval - ability vs achievement + dyslexia screening. We found out that she has a disrepancy in associative memory vs her overall intellectual ability. It's a significant discrepancy - almost 3 SDs. The impact of having a relatively weak associative memory meant that when she learned the alphabet, learned to read/spell words etc she didn't remember things easily that related to the skills needed for reading. We (parents) thought it seemed like she had trouble with phonics, but her testing showed her phonemic awareness is actually incredibly high - so that was a surprise!
FWIW our older dd had trouble learning to read to, very similar, and in her case it was a vision issue - she had extreme double vision and one eye was shutting off, plus tracking issues. Vision therapy really helped her though.
We went back and forth trying to decide whether or not we should have both dds privately evaluated and ultimately were very glad we did - for both. DD7 did go through an eval by her school's reading specialist but they felt everything was "fine" since she her reading achievement tests were all at grade level. Oddly enough, they weren't all on grade level in her educational eval!
Best wishes,
polarbear
