Main bearing knock was an issue with the 4.1, 4.5, and the 4.9. But it was an easy fix, and no special tools were required. This knock generally occured when the engine was at operating temperature and at idle in gear. Noise at startup would likely bec caused by something else, like oil drainback after shut off. I have performed this job many, many times. part of the procedure was to check clearances before the new inserts were installed. In every case the clearances were within spec. Then you rolled in #1 and #5 inserts, torqued the mains then rolled the engine over by hand to make sure they were not too tight. This fixed the problem in every case.
Also, the 4.9 is of the same engine family as the 4.1 and 4.5. It is not a differant animal.
I have spent some time thinking about this problem. I don't know if my theory is correct, but it makes sense to me. The block is aluminum, the bearing caps cast irion. Aluminum has a very differant expansion rate than cast iron, and hence expands to the point where the clearances can increase where the crank can float causing the knock when the cylinder closest to the bearing fires. Also, this was not generally regarded as a detriment to the durability of the engine. Bearings that I removed showed no excessive wear.