You are correct allocating by days or pay periods assumes the pay is relatively the same each pay period. The most accurate, if the information is available, is, as you mention, to use the actual paystubs and allocate those according to where you were when you received them.
Typically, a W2, date of move, and pay period length (weekly, bimonthly, monthly) will be the information available to you and the taxing agency will only have a W2 and the dates you provide. A taxing agency will generally use days to allocate and if your figure is reasonable, you will be good. If your figure is way off, you will just need to be prepared to show how you calculated should it ever come up. If you can show uneven pay with the bulk of pay in another state, for example, that will work.
The allocation just needs to be logical for your situation.
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