That is something that doesn't usually happen, especially after a fresh repair. Sounds like either improper installation or a defective chain. Did you follow the instructions letter for letter when setting the valve timing? I'm almost sure since the engine fired right up when you finished it. Just have to ask though.
If the crankshaft was bent, the engine would run bad, have a knock, and have low oil pressure just to name a few things. Sounds like you may have gotten a defective chain or have a problem with gears. One of the components that the chain drives, may be seizing intermittently
The rough idle could have been caused by a vacuum leak or improper installation of the chain, provided there is no knocking. Too much play in the chain will retard valve timing and the engine WILL run, but won't make much power at all until it reaches higher RPMs. Eventually it will become so loose that it will slap around and could possibly break.
Another point is, on alot of engines the tensioner and timing gears should be changed as a set on a chain driven valve timing setup, when servicing the chain.
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