Bought a '99 Outback...a few questions/concerns

Bought the car on eBay a few weeks ago. Drove it home 300 miles with no issues. It has a few bugs to work out though. If anyone has any suggestions, please chime in.

'99 Legacy Outback Limited wagon, manual tranny, 210k on the clock.

First observations:

- CEL is on, but car won't communicate with the AutoZone reader.
- The exhaust system has a leak.
- Engine has a miss during acceleration (especially when cold). Wires look new, pulled the #1 cyl plug today and it looked fine. Coil has no signs of corrosion on contacts.
- The idle fluctuates after a cold start and doesn't level out until a few minutes later when the RPMs drop to below 1k.
- When the motor is running, I hear a loud hoot/howl, its vibration can be felt when touching the airbox. It gets much louder once the airbox cover is open. Is this normal?

Thanks for any suggestions.

Jim