How to take apart the straight six without destroying anything

4.0 L engine is likely the last easy engine to work on. Get a haynes or chilton manual and follow the directions. In order not to destroy anything, that lies with you. Use care, don't force anything and use the proper tools.
As far as "taking apart" , some items such as the crankshaft are not removable without taking the engine out. A carefully torn down engine should need no more than replacement of worn or damaged parts and a gasket set (plus machine work where necessary)
Any questions about a specific component can easily be answered by anyone here.