Check the alternator using the electronic odometer trick so you can monitor voltage while you drive. Key off, press and hold the odo reset button. Turn key on, continue to hold button until odometer display reads [test]. Release button, now each time you press and release the odo reset button you will scroll through one of 30 test functions. Look for the one where the display reads [bat 12.1] or whatever your voltage might be at that time. The display will remain in test mode until you turn the key off, so you can start the car and now you'll be monitoring alternator voltage. If your alternator voltage reads 14.9v or more, then you need a new alternator. If it reads less than 13.2v, you need a new alternator.
It seems to me that your problem is vacuum related. You found the PCV, that is the most common vacuum leak or problem, however there must be some other leak somewhere. Also, once you do find the problem, it might help you to reset the A/F ratio- which the car will do anyway over time, but you can force it to do it faster. Disconnect the battery for 10 mins, I do this on a warm engine, now reconnect and start the engine. Do not touch the accelerator, and allow the engine to idle for 6-7 mins. During this time you will notice a slightly higher idle than normal- around 1k rpm. The idle will fluctuate slightly, but after the test is complete, the idle will drop to normal which is around 700 for both transmissions.
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