My opinion (which differs from OBGs) is that there isn't much wrong with re-using both the inlet and exhaust manifolds straight from your old KY engine.
The inlet or exhaust from a JX is not really suitable for what you want, as it was designed for a turbo.
In the end it all depends on what you want to achieve.
The advantages of OBGs setup are that you will get a small amount more power at high revs due to marginally better gas flow. The disadvantage is that it will be considerably noisier due to the cone type filter in the engine bay without noise attenuation. There may also be a risk of water getting breathed into the engine due to the position of the air intake. You will need to get a custom exhaust pipe made up from the exhaust manifold to the silencer.
The advantages of re-using your existing manifolds from the KY is that the engine will be much quieter, (as long as the original systems were complete and leakproof) and that no special parts need to be made. Against that, you will have a slight reduction in power at high revs (although I can't say I've ever noticed that) It is also advisable to slightly modify the fixing holes of the exhaust bracket and adjust the fitting of the downpipe into the silencer, as the 1Y engine is a smidge taller than the KY.
For more information have a look at this thread
http://www.brick-yard.co.uk/forum/1-6cs ... KW=#413096" onclick="window.open(this.href);return false; which has sections on inlet and exhaust systems. It's about the AEF engine, but that is so similar to your 1Y that it makes no difference.