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Both are grammatically correct, but they could be interpreted with very different meanings.
The first one is the one you want, I'll wager.

Regards,
A-

Could you tell me what the difference is, AS?

If I read your book in three days, I would be surprised. - It can be interpreted this way: If I start reading it now and finish it in three days, that would surprise me.

The first option is much clearer because there is only one interpretation.

Regards,
A-

But you won't find such contiuance in, say, 'He'll be back in three days' or 'I'll call you in two hours', will you? If not, could you tell me why not?

That's true.
The phrases be back and call are one-time events and, unlike read, do not have any implication of occuring over a period of time. That's why I said there was the possibility of misinterpretation.

To be absolutely clear, I would use the first sentence, even though both are grammatically correct.

OK. Thanks, AS!