When you took it back to the shop that did the work, what did they say?

 

The independent shop was local. The H-D shop was was while on a bike vacation away from home. No chance getting back to that dealer and I don’t trust the local independent shop to make things right.

 

is the clutch out of adjustment?

 

This doesn't make sense. Replacing the inner primary is a simple job and has nothing to do with with the drive belt or the rear wheel. I'm assuming the bike has an auto tensioner. If so, it should've gone back on in the same position it came off. As for it "needing more power" and sounding louder, is it possible the clutch is slipping? They were supposed to adjust it when they put the primary back together. That would be the first thing I would check. And don't ride it anymore until you get this sorted out. Adjust the clutch and inspect and (if necessary adjust) the drive belt before you roll another wheel.

 

They did adjust the clutch, I will check that out. Lots of vibration now when you ride it.

 

Vrod,
I would take it back to the Indie that did the original work and complain.
I would not tell them that you took it to the dealer.

I know this is of no help to you but I'd offer a little advice to others.

My story;
I'd known for at least a year that my Dodge Ram heater core was clogged and needed to be replaced.
So a week before my summer vacation I had some free time so I decided to swap it out.

Everything went well with the swap.
I test drove the truck for the next week without any issues.

We then took off on vacation which was a 9 hour drive in the truck pulling a trailer with the bike.
About 4 hours into the trip my truck just shut-off going down the highway.

It wouldn't even turnover and sitting on the side of the highway there was only so much I could do.
I called for a tow and had the truck towed 45 miles to a Dodge Dealer.

Long story short; a day and $1400 later we were back on the road.
What had happened is when I put the dash back together after the heater core swap I apparently didn't get a major electrical connector fully seated and it had come disconnected.

The dealer had to pull my entire dash back out to reconnect it.
As we know dealer time is not cheap.

I learned from this that prior to going on any trip; never do anything to a vehicle that's not necessary.
I had been driving with that clogged heater core for a year and at 90 degrees outside heat certainly wasn't needed on this trip.

I should have waited until I was back from the vacation to tear the dash apart.
Then the loose connector would have only cost me some time and a tow.

Instead we were out about $1600, lost a day of vacation and added unneeded stress at a time where-as we should have been relaxing and enjoying life.

 

You didn't say the year of the bike, but I'm going to assume that the chain is not self-tensioning. It also sounds like the belt is not properly adjusted. I can't tell you how it got that way, but it's easy to check. Get the belt tension measurement tool from any dealer. It's cheap. Measure the tension yourself. Measuring the primary chain tension is pretty easy, too. If it is self-adjusting, skid this step.
At least this way you'll know if anyone is BSing you.

 

The belt squeal and wobble is more than likely that the rear wheel is not in straight/aligned. So check clutch adjustment and make sure rear wheel is even and tight.