The higher output Valkyrie alternator is the better choice of the two.
Not in my experienced opinion. Though I haven't tried the rewound alternator, this one is MADE to produce 90 amps (1325watts). Didn't bother me to mod the frame to pass it into position, since the alternator already fit the engine, and the frame is overbuilt, can withstand a little less meat at the swingarm pivot.
I wonder how the necessary Compufire modifications to the bike frame and motor housing will affect the longevity of the bike, notwithstanding the effects of the elements from inclement riding conditions.
Of course I recognize the bragging rights of having a Valkyrie that can power a dozen homes at night.
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I did this mod in 3/2002 and am still riding the same bike more than 50,000 miles later with no adverse effects: no problems with the frame or motor mods. Am presently running a 400watt amplifier, aircraft landing lights, 130/90 headlight and 2 more 55 watt spot lights, lots of other lights though most are LED's so they don't count; GPS, heated jacket and gloves, piston compressor with active air suspension (I dial it up & down frequently) & large air horn (and infrequent tire fills), and pager alarm system. Installed digital voltmeter and monitor it all the time - it's usually at 14.4v even at idle - the lights don't dim when the bike is idling. The install did require a larger fusible link - 110amps - and larger battery - I used a Yuasa 21 AH Gold Wing battery and modified the battery tray so the battery and amplifier fit there. I never run low on juice though I wouldn't claim this is any bigger than a car alternator. In fact, that's what it is - a Delco car alternator with a housing made to fit the GL1500 engine - though not the Valk frame.
I'm thinking about installing a road de-icer...