My 2 cents- Engines that sit
and just get reinstalled, coupled with a flush, need to be run back in. Even the BMW owner's manual says to occaisionally run it hard BEFORE going in for a service. Just starting it up and idleing won't do it. Go beat on it, rev it up, run it on the high way, give it lots of italian tune ups ( no offense to the Italian constituancy) hard down shifts. Buy some techtron at Exxon or Porsche dealer, otherwise known as top end cleaner. Seafoam it, slowly. Find out which cylinder is doing it and concentrate there. Smoke it up or break it is my prescription.
Said another way- the enigne gets junked up, never gets hot enough to burn off deposits on the valves and combustion chambers, rings, etc. I've seen cylinder compression go from 120 to 170 in a M30 that had been sitting or only idled by grandma driving habits :shock: so they can be pretty bullit proof.
Since you didn't post a picture, let's also assume you don't have the valve cover vented to the carbs, emmission control equipment, etc that's doing something wonky. The engine is realitivy clean, no oil near / near vacuum leaks. The intake manifolds/ nuts with just wave washers can be loose so go back over the carbs, etc.
Since you said it idles, I assume reasonably ok. You changed the oil- what weight? Terribly important to use a corrrect heavy weight. Happens all the time.
Adjust your valves. What did the top end look like?
What do the plugs look like? What kind and heat range of plugs?
What year is the head? Has it been replaced already?
Don't get me wrong, if it's purely mechanical wear then it's got to be fixed or replaced.
Yep, you can bolt up a later 3.5 with the carbs you've got.( Check the right side motor mount on the 87 for both mounting positions so you don't have to buy/ fabricate an adaper plate.
But usually, unless you're rebuilding it or at least refreshing it, you're just switching out to new problems by dropping in something used unless you absolutely know the condition beforehand.