I hope this is the right place to post this....
What is the story when you look at a transom assembly and you see a plug has been put in near the top right side of a transom assembly - about 1" or so in dia.?
I know it is a method of fixing something that has wore out but I need this explained to me so I can understand what has been done, etc. Thanks!

It's Mercs way of accessing the bolt and nut needed to remove upper swivel shaft. Probably had gimble ring replaced or repaired.

So should a fella run away from transom assemblies that this has been done? do you have a ballpark idea what standard B1 transom assemblies that this has been do to are worth?
Thanks in advance!!

I would say it depends on who repaired them and how long ago. I wouldn't give more than about half the price of new.
New complete transom assemblies can be had for around $2200-2400.
Yours should be HP transom assemblies also.

This is the JRmarine way. http://www.jrmarine.com/instructions.htm
Merc has a kit as well