TD42 engine knock

Hi all, this is one of my first posts so please excuse me if i have placed it in the wrong area of the forum. My 2002 gu td42 has recently developed a knocking sound in the engine which has me a little puzzled. I assumed it was a big end bearing so i went ahead and removed sump and the big end bearings hoping there was minimal if any damage to the crankshaft. There is some wear marks on the bearings but not to the extent i would think could cause the knocking sound. Interestingly though the bottom bearing on 4 of the 6 cylinders has noticable wear in the centre of the bearing shell where as the top shell doesnt display the same wear characteristics as in there are no marks in same place as the bottom shell. Can somebody tell me why this would be the case. My next plan is to remove main bearings and i am not sure if i can do this with the big end bearings already removed in case the crankshaft moves out of the position it is in and puts timing out or something similar, or if that is even a concern. Any ideas or answers would be greatly appreciated. By the way it has 320,000 kms on it. I would put some pics of bearings up but i dont know how to.