Just finished an engine swap on my old carbed 2.6 Raider up to a fuel injected turbo 2.6 running my Megasquirt system. Fired up like I never had the engine out but noticed I was not charging (same alternator I was running that was great). Swapped out to another spare I had, still no charge. I've traced all wires from the alternator post to the battery terminal including the fusible link and that side is all good. Trying to figure out how to check the wires from the alternator plug (although I guess one is tied to the idiot light in the cluster which is staying on of course). While there is always a chance I have 2 bad alternators (given both worked fine when removed) I want to confirm everything else before pulling another alternator.

Any ideas or advice?