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On the crank gear, which side goes against the crank? the side with the ridge or the undercut? With number one at tdc where should number one intake be?
The bevel goes back against the crank to allow for the fillet radius where the snout of crank is machined. Should be a timing dot on the other side to line up with the dot on the cam gear.
Don't worry about valve position at this point. Line up the dots with crank gear at 12 oclock and cam gear at 6 oclock. That will have #6 at TDC compression and #1 with valve open on overlap. When you turn the crank one turn and the crank gear is at 12 oclock and the cam gear is at 12 oclock you will be on #1 TDC compression stroke.
On the crank gear, which side goes against the crank? the side with the ridge or the undercut? With number one at tdc where should number one intake be?
I don't understand the question. Your crank and cam gear should have a dot on one side,like the timming chain gears. Gear sets come with " buttons " to set cam advance or retard, shims and a large cam button to keep gear from hitting timming cover. Some gear sets won't work with stock timming covers. Also some require some grinding of the block. Not sure what you mean in second question. At TDC, both intake and exhaust valves will be closed.
Good luck.