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If no vibrations before, then it most likely is whatever you did, tuning may or may not help.
If you are modding your baffles, I would instead get new slip ons at a minimum - used ones are dirt cheap and would be much better than some homemade baffle mod.
If you can afford it though: a new complete exhaust, air cleaner, and a quality tuner like PowerVision would be a great upgrade.
I took my S.E. mufflers off and replaced them with the stock muffs, which have removable baffles. Not going to spend 500 bones on a tuner without knowing it will cure the problem. My mechanic only charges 65 an hour.
I will bet my last dollar, that the collars are not torqued to spec, I had many a vibration problem with mufflers, I went through all the bolts and torqued them proper, and vibration was gone, and if you played around with the heat shields, you will see the slightest variation in putting them back in the same place will cause vibrations, I have been there and got grey hair but finally got it sorted.
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