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...Alternatively, would a relay work? And would I be able to switch that on and off remotely without risking damage?
A 200A relay (rated for 120A continuous) could be bolted more-or-less directly to the alternator's B+ terminal and would cost about the same as running a new cable from alternator to battery and fitting a manual disconnect switch.
The use of a relay there, provided it can be used safely, also gives the potential to switch the alternator on and off automatically in response to events like braking or slowing down on engine with zero fuel being delivered. Or even if I had to operate the relay manually using a switch in the cabin, it would still be very useful to be able to switch the alternator output on during long hill descents.
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