Here's what I've researched (notice some may be here say as you can't believe everything you read on the internet):
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The breather re-route should not hurt your engine as far as crankcase gases no longer being drawn into the intake - even cars before emissions were in place, just let crankcase fumes/pressure escape to the atmosphere.
However, the vacuum produced by the intake will create a negative pressure environment in the crankcase and help evacuate gases and moisture. Additionally, depending on how much vacuum exists, the rings *could* seal better, leading to less blow-by.
Another method used to create negative crankcase pressure is by placing the vent into the exhaust at an angle, where the passing exhaust gases pull the garbage from the crankcase via the venturi effect. Notice that in this case, an oil mist/air separator is used to prevent oil from entering the exhaust system.
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Over the weekend I have decided to leave the vent going to the intake, however I have added an oil-mist/air separator and catch can (which I have might have to improve on a bit) between the vent and the intake, much like pamver posted a few posts ago. I have left both lines going into the intake, but added a much less restricting filter to each hose. I will be checking these two filters to see how well my solution is doing by catching the oil-mist.
A write-up with pictures will soon follow in a new thread.
*Flame-suit on*
Ben K.