My 2 cents, never having rebuilt a B16 engine.
You must chase (run a tap down) to clean up the holes. You must also chamfer all of the holes. This removes the threaded part of the hole that is pulled up when the studs were tightened.
And I would go with new, hardened studs rather than cap bolts if at all possible. There is a reason they were used in the first place. Studs allow a much more accurate torque value and don't "walk" when being tightened. Google "engine block studs versus bolts" and you should come up with several hits worth reading.
Studs and bolts tend to stretch when tightened down more than a few times, so check for stretch if reusing your existing studs.
Also, don't bottom the studs in the hole. Leave them 1/4 to 1/3 of a turn loose.
If the engine is out, even if you don't do any machine work, you might consider doing a refresh, with new bearings, cleaning the oil galleries, new oil pump etc.
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