how did you determine 3 & 4 weren't firing?
Fuel, air, spark, and compression are needed to fire - you say you've got compression verified which indicates the rings and valves are OK in 3 & 4. If the engine is running on the other cylinders, then fuel and air are verified in a general sense.
1) It could be ignition.. have you confirmed spark at the plug for both cylinders? That is: pulled the plug and ground the housing and seen a spark?
2) If there is spark, then it is timing or firing order which ApacheFiend suggested
3) A cylinder filling issue, which could be a blockage as you mentioned. However I would expect that to show up on your compression test.
4) your compression test was faulty (gauge or method, etc) and you really don't have good compression in 3 & 4. If you didn't indicate that compression was good in those two cylinders, i'd tell you to check the head gasket between 3 & 4
good luck
