Best way to check for a spun bearing is to drop the oil pan and manually inspect each rod to see if it is able to move around on the crank. It should be pretty evident if you spun a rod bearing as that particular rod should move back and forth on the crank journal and this is what causes the "knock". All you'll be out is some time and an oil pan gasket and oil change if that's not it.
Most likely you have spun a rod bearing as that is the main culprit in these engines. As far as where the oil went, have you been checking under the car to make sure you don't have a seal that's started leaking? Otherwise it could possibly be a head gasket that started to go, but you should be able to look in your radiator overflow tank and check to see if you see any oil in the coolant as 3 quarts should show up there if that's the case.
Your options run like this- rebuild your current shortblock, buy a used shortblock or complete engine in good condition, 3 liter. Any of the above options is probably going to run you close to the same amount in parts and labor for the actual swaps. Your rebuild is probably the cheapest, used engine, the next most expensive, and the 3L the most expensive, but you're getting a rebuilt engine with more power at the same time so it does balance out in that respect.
If you've spun a bearing, then you are almost certainly going to have to pull the engine due to damage of the crank journal and it will have to be polished and/or ground.
Hope this helps,
Rick
PS, drop me a PM if you need any additional help or want to go with a 3L.
