If these are both Bosch type alternators with internal regulators, nothing will blow up providing it is wired up properly. The electrical system is "protected" by the internal regulator of the alternator, the regulator would have to fail shorted to pop a battery or result in electrolyte boil-off (a very bad situation).
I suspect your biggest issue will be mechanical fitment... assuming that the alts have different style housings.
To fully take advantage of the additional charge current, consider going with an Optima battery which has higher CCA ratings than standard batteries. As far as gas mileage goes, I doubt you will notice a difference as the mass of the armatures is roughly the same. In general, if your car normally gets 30mpg and you make the same run with a drained battery, you will not get 30MPG until the battery is charged back up... the difference will be small though.
One thing I would recommend though is to inspect the red alt cable running to the battery as it will be carrying a higher charge current than it was designed for when the battery is drained. Check for corroded connections and cracks in the insulation, clean / replace as needed. Also inspect the ground wire that runs from the alt to the engine mount, clean/replace as needed.
jorrell
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92 245 250K miles, IPD'd to the hilt, 06 XC70, 00 Eclipse custom Turbo setup...currently taking names and kicking reputations!
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