1994 Dodge B250 Timing problem?

Hello, I have just replaced the timming chain on my 3.9L engine because of to much play and chattering noise. I placed the #1cyl at TDC on the compression stroke and lined up the Cam and Crank marks as per specs. When I took off the distributor cap, the Rotor was pointing to #4cylinder. I rotated the cam around again to make sure the valves were in the compression position and they were. So I removed the distributor and rotated it to the #1 position and tried to start it. After several attempts of cranking it would not start. I then rotated the distributor so the rotor was again pointing to #4cyl and it started right up. Using the timing light, the marks are not even close! But the vacum gauge shows everything is normal. The problem is that while the engine does not hesitate or miss fire and runs quite well, there is a bit of roughness sort of like a shutter or vibration you can feel at 30mph and above. I'm quite sure it is from the engine. Any ideas on this would be appreciated