Langdon, the problems you are having with Molly are not things she would pass on to a kid. If it were undershot jaw, or a dreadful deformity, then I would agree, don't breed. But you have a lovely goat there, and of course you should breed. She is nearly identical to our Molly goat, and she has given us two lovely kids so far, so go for it!! You are very caring with your goats, but you must stop worrying, and enjoy them!!
If the goats are ill, of course have them treated, and do general worming, foot trimming, de lousing etc. but a lot of the things you are finding wrong, such as the itching, are something goats do, and have to put up with. Oops, did not mean this to come out critical of you, because you are doing everything right, but its not right that you seem to be spending so much time worrying - if you see what I mean. And for all this to make you consider not breeding from Molly, you must not let it stop your breeding plans!!
Re the excema, this is probably due to the winter weather and is still there. When its muddy and wet, goats can get serious foot problems, but if Molly is not lame, thats not too bad. If she is seeing the vet, let him see it, he will probably give you some spray in a yellow can, its blue, and very good indeed for foot trouble, but only obtainable from a vet, and about a tenner.
Are you seeing the vet with Mollys udder problem?