Thats a good sign that the engine is ok.
As for the smoke and rough running, either you have an additional injector that has failed or the one that was replaced was the wrong one...
There are 2 different injectors available for the 5.9 engine Standard output and High Output. If the wrong one was installed it can cause rough running and excessive smoke..
Many times when an injector fails in a 5.9 they can keep failing one after the other especially if there has been contamination present at one time or another (water, dirt, etc). When the number 4 was replaced was there any rust present on the connector tube? If so, It means that there is rust on the rest of them and you will need to replace all injectors to solve this issue.
If you need additional information, don't hesitate to ask, I am happy to help as long as necessary to help solve your concern. Remember, a "Positive" Rating will not close this question, You can post a reply here whenever you want, even after rating my answer!