Raid,I thought it interesting that the two Canon 1.4 lenses appear to exhibit a slight difference in contrast. Assuming that all other factors are the same, the "98" lens appears to render higher contrast. Of course, a miniscule sample doesn't say much- I just find it interesting.
I would bet that a good cleaning of the J-3 would cut down on the flare significantly- a bit of oil on the lens elements would contribute to the flare.
Also, agree with an earlier poster- I don't think that there are any focus issues with the test.
Looking forward to the rest of the pics.