Often overlooked is the mechanical condition of the engine. Even though you replaced the long block there could still be issues. I would recommend starting with a compression test and if you find low compression in one of the cylinders, follow up with a leak down test. I would also recommend checking the timing components to make sure they are secure and in time. If you’re off a tooth, or if the timing components are loose it can cause a misfire. That way you can rule out a mechanical issue as the cause of the problem.
More info here: http://www.ericthecarguy.com/faq/solving-automotive-performance-issues
Good hunting.