What does a uncentered speaker sound like if you refoam and don't get the cone centered.

It will throw off the proper pistonic motion, which is never really perfect to begin with. In other words, the sound wave propagation will be distorted.

Try pressing with thumb and middle finger using both hands,basically four corners of a square on the cone ..equal pressure on the four points ...down with light pressure moving cone in and allow it to move back...do that a few times and if you feel rubbing its messed....the rubbing will sound like distortion  when audio is run through it....if you redo it again use shims so coil is centered.

I can not get the center dust cover off.. I tried a very sharp razor knife and its not cutting it. I can just cut it off but I wanted to reuse it. Too scared of cutting the cone.

The cracking sound you’re hearing is the voice coil banging into the magnet and pole piece. The voice coil gap is very tight. Two things hold the coil in alignment- the spider, and the surround. The spider is the big accordion looking thing behind the cone. The surround is what you messed up. When you glued the cone off center you also caused the coil to be out of alignment. It is okay and has enough clearance, until it starts moving a lot with powerful bass. Then it scrapes and makes that sound.

If you haven’t abused it too much already you might be able to cut the surround and re-glue it properly and save the driver.

Do not cut the dust cover. Behind that is the spider, the one thing that is still in the right place. Lose that and you are screwed. Whoever said to cut the cap is telling you how to destroy it for sure.

I've had to remove new dust caps to add phase plugs. Talk about sweating bullets. I managed to do the job but you see where the old cap was. Performance wise adding the phase plug was a big improvement.

I've removed a lot of dust caps and replaced them. I've added inverted caps, sealed for phase plugs and added cone phase plugs attached to the cone vs stationary phase plugs.

It can be unsettling to take a modeling knife to a cone, BUT that is how it's done.

It does take a bit of surgical skill. A good firm grip goes a long ways..

I know this sound weird, but if it rubbing just slightly, sometimes rotating the driver and putting the widest part of the gap on the bottom and the narrowest on the top, helps. The weigh is just enough to stop the VC rub. 

I'm also assuming the driver is mounted in a vertical baffle face.

All that said, the best solution is to redo the surround, if you think it's rubbing.

Are you sure you didn't get any debris in the VC cavity when cleaning off the old surround? Take the driver back out and give it a good shake to get the crap out and see if it's centered.. Check your work.. pretty easy. 

Make sure there are no air leaks either soft seal the drivers. To find the noise use a hose and put it to your ear and listen. Be surprised what you can tell with a stethoscope. Same with box leaks. Listen around the seams and seal..

Regards