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I have an SD card that will only store files of 512, 1024, 2048 and 4096 KB in size. I wanted to set the allocation unit size to 512KB, but the maximum allowed in Windows is 64KB.

Can I set this limit of 64KB higher in either Windows or Linux? I doubt it will make a giant difference, but every little bit helps.

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The allocation unit size will make very little if any noticeable performance difference here. Too large of a size can lead to inefficient usage of storage space if you have many small files. Stick with the default and let the SD card controller handle block management and buffering -- that's what it's there for anyways.

The way to get the best performance and reliability is at a higher level, during actual data transfers; e.g. when copying files use block sizes that are multiples of read/write block sizes (although usually you're limited by e.g. USB adapter interface transfer rates or whatever anyways). Note that SD cards can have different read / write / erase block sizes. You can also use programs like these or TeraCopy, all of which provide better performance and flexibility than the Windows default copy / move.

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