Aloha all.
This is my first post.  Having a hard time diagnosing a couple of issues.
The first is a rough idle.  Its not a constant rough idle. It happens often but not a constant rough idle.  It has stalled out a few times recently.  Has a slight loss of power.  Has stuttered a couple times while at higher speeds.
The second is a rattling noise that only happens for literally a second when i first start the car. Then a similar noise happens when I hit 1500-1900 rpm.
I have changed the fuel filter and spark plugs. Cleaned out intake manifold and egr valve. cant blow through egr valve. So supposing its still good. 
Thank You

Have some one start the car whilst you're stand in front with the hood open - try to see if you can find out where the noise is coming from.  The 1.8 uses two timing chains which are at the very front on the engine and are known to rattle on a cold start - it's a good idea to get the chains fixed ASAP because if they fail you'll probably end up with a damaged head, pistons & valves.

It's also possible for the serpentine belt idler & tensioner pulleys or the fan pulley to make a noise at start up - so I would suggest you remove the belts and spin the pulleys by hand, they should spin smoothly & silently, any noise, any roughness is a sign of a bad bearing - the bearings in the idler & tensioner pulleys are replaceable - you can also start the engine without the belts to see if the noise is still present, just don't run it for more than a few minutes.

Thank you for your quick response.  i'll check that out tomorrow and get back to you.