You must be new to cars. Let me help you out a bit as I know I struggled for a while myself. As much as you think you have a unique issue...when a car has been around for 20+ years, a lot of the known issues and problems have happened already and threads are out there telling you how to fix them. Just keep that in mind next time you're bummed the answer doesn't pop up in the first two Google search results.
1. Hmm well if the noise has happened with all configurations of your parts, I would then start looking at what hasn't been changed out. I know some of the short throw shifters can buzz, might be worth looking into. I don't have much experience with weird drivetrain noises that likely involve the transmission.
2. Oil leaks are easy man. Go to rockauto.com and order your front main seal, rear main seal, new valve cover gasket and reseal your oil pan while you're at it. Sounds overkill but when the car's down for the clutch job, might as well nip some other maintenance jobs as it is indeed a ~20 year old car and those should be or already have failed. You can then narrow the leak down better after you eliminate the basic leak prone areas. Also look at the stock oil pressure switch on the block located near the oil filter, as this is prone to leaks as well.
Oh and dark oil is nothing to be concerned of, that just means your oil is likely doing its job. Now if the oil is pitch black or near it you may have an issue.
3. Courtesyparts.com is a good source of OEM Nissan part number references and a place to purchase them.
http://www.courtesyparts.com/240sx-p...3826_3828.html
Honestly you should really read into how to maintain a car. Not trying to insult you but it really sounds like you need to understand the basics of car maintenance and how to answer these questions yourself. Good luck dude and I hope this is of some help. In the future, don't forget we have a Small Questions Thread if you need more help.