It is my understanding the answer is "When it no longer has a Lycoming or Continental Data Plate." But you would do better to talk to your local FSDO about their interpretation to that question.
Using Automotive spark plugs and an automotive harness to adapt to them would exempt you from a spark plug or ignition harness A.D. since there won't be any out there against the automotive Spark plugs. An aftermarket or home brewed exhaust would exempt you from an A.D. against that exhaust; again because there won't be an A.D. against a non-TSO exhaust system. But, just because you have an aftermarket or home brewed exhaust doesn't mean I wouldn't look at it for problems and recommend fixing it if there are problems. Same is true for your home brewed oil filter assembly. The alternator is part of the Airframe accessories, so that doesn't apply since we're talking Engine A.D.s and your E-AB airframe sure isn't going to have any A.D.s. But if you had an alternator that had known issues, I'd certainly bring it to your attention as well.
IMHO, Certificated engines do exist in the Experimental world. The FAA recognizes such, which is why you can have a 25 hour phase 1 test period if you use a certificated engine/prop combination on your E-AB aircraft. That is exactly what I did on one of my E-AB aircraft. The engine and prop were in the same combination as they would have been when installed in a certificated aircraft. The engine and prop both met the standards for their individual Type Certificates (including STCs) when they were installed into my aircraft (although I completed a field overhaul to new standards prior to installation). IMHO, if the engine is built and maintained in compliance with it's Type Certificate, then it is still a certificated engine. As such, I would have no problem with mounting it back into a certificated aircraft. I keep seeing people stating otherwise in the forums, but I would respectfully disagree. If it meets the standard of it's type certificate, it can be used as such.
So let's be clear about something here. There is what you may be able to get away with legally, and then there's the issue of asking a mechanic to put his license at risk by signing for an engine that's not up to snuff on it's A.D.s. Those are two different subjects. I've never had an owner offer to indemnify me as a mechanic if the FAA decides they don't like something I signed for, and I don't get to go back and bill the owner for the time I'm going to waste dealing with the FAA because the owner didn't think complying with A.D.s was a necessity.
FWIW, I was wearing an airplane builder hat some 30 years before I got my A&P hat, so I believe I do see both sides of the coin here. For the purposes of this discussion, I've been wearing my A&P hat since the discussion started out with Tony's favorite subject of bashing us ignorant A&Ps.
But I must admit, I have had problems tying my shoes in the morning since acquiring the license.
-Cub Builder
A&P, Former EAA Technical Counselor, Former EAA Flight Advisor