1951 Johnson TN27 Motor

I just picked this motor up today for a low cost. Evidently this motor was worked on at a Marina in 2006 which costed about 450 bucks. Part of the process involved a break in period.

My question is, what was most likely done to the motor at that cost and requiring a break in period?

I am trying to get this motor running, I can get it going but its running rough and Im not sure how to make the proper adjustments to make it run smoothly.

Can anyone offer any advice on this?

Break-in period sounds like they rebuilt something internally, maybe rings? Hard to say.
Static setting on the jets is 3/4 turn open on the high speed jet and 1 1/4 turns on the low speed jet. That should get you running and then final adjustments in the water.
Here's a good link on the carb itself...
http://www.pochefamily.org/outboard/CarbService.html

I tested as much as I could out of a gas can full of water. I had to put it in the water to see where I was at. After getting it in the water, I had a hell of a time getting it to start. I actually gave up and used the oars for a bit while I was discouraged.

I went back to it and readjusted the settings and was able to get it to start. Once I got it started, I was able to figure out how to adjust the lean. After that, I was able to get it to start on the first pull every time after it was warmed up.

Its a hell of a motor, I was surprised at how well it operated once I was able to get it up and moving.