I, too, have a 4100 and have some problems with certain implements having too wide of spacing causing the rubbing on the tires. I did notice one thing looking at the pics which would help you out in many ways- Your rear tires are on the narrow setting! You need to turn them around (and change sides, of course) and this will increase spacing and give you much needed stability. Stability is important with a cutter because it is a relatively heavy implement and you tend to use them on uneven ground where it can swing side to side with a lot of force- So turn those tires around to wide! Also- The turnbuckles tend to be wimpy and will bend if you don't tighten them up after hitching something up so there isn't too much sway. I know that ideally some implements should have more sway and others less but I have found you need to tighten most everything up on the 4100 because if you are using a heavy implement and it sways back and forth those turnbuckles WILL bend. And yes, you can turn the pins to the inside if needed (I did it on my disc harrows) but try moving the tires first and resolving the turnbuckle issues.
Also- Looking at the pics it appears you need a longer length top link for this particular implement. You are using the JD orig. link and it appears to be turned all the way out and you still don't have the proper geometry for the cutter pivot. I'm sure you noticed that link is easy to wiggle around like it's going to fall apart when it is extended as far out as yours is. Find a longer length top link (I bought one from Agri-supply for about 15.00- can't remember the exact length but I bought the longest of the 3 cat. 1 links they offer). I have found I need the longer length link for some of my implements like discs, plow, and blower. For other implements I go back to the stock link. Just depends on the geometry of the implement.