you mention "removing the magnets in favor of a ring magnet"
does the alternator have a stainless steel shaft? probably not seeing how one would not be strictly needed if the rotor was fitted with individual magnets, however
if you have a standard steel shaft, and are using a ring magnet, most of the flux path will follow the path of least reluctance! guess where that is?
yup, it will route through the shaft, the shaft effectively becomes a magnetic shunt in the flux path and you don't get much across the airgap cutting stator windings to make power.
check that shaft, and see if a magnet is drawn to it, if so it is steel, if not or very little then it is stainless and all i have said is of no use to your problem.
i am not familiar with your alternator choice, but given the price of most of these converted units, it is unlikely the manufacture replaced the shaft with a stainless one when the only need would be one of corrosion abatement.
+1 on going the whole distance with 2inch pipe, you have a pretty long run and likely are loosing some power to pipe friction in my opinion.
fwiw
bob g