1. your clutch shudder could be caused by a number of things. These include worn out front or rear engine mounts, dry or worn clutch thrust bearing, dry or worn clutch release bearing, damaged or uneven clutch friction material, uneven surface on flywheel, air in clutch fluid or and a number of other things.
Try bleeding your clutch slave cylinder or completely replacing the fluid, check all engine mounts (particularly front and rear) but if you want to go further than that you'll really need to take out the transaxle, which is a lot of work.
2. The whistling noise could be an air leak as you say - try revving the engine by turning the throttle lever on the throttle body and listening for the noise in the engine bay. Run WD40 around where you think it is and see if it "sucks it up". If so, you've located the problem.
3. The loud ticking noise is usually caused by one of two things - the hydraulic lifters or the fuel injectors. If you have a CA20E powered car it could be incorrectly adjusted valve clearances. Try to isolate where the sound is coming from, whether it is only idle, low, mid or high rpm, and what general side of the engine it is coming from - it will make it a lot easier for us to help you.