Audio_girl,
Excuse me, but since I don't know you or your experience level, I have to ask:
Did you use all the same power cords, interconnects, and speaker cables when you performed your evaluation? Or, did you try different things to try to optimize the performance of each amp? Were they plugged into the same AC line? Through an AC conditioner or not? Did they use the same mechanical-coupling methods or vibration control? Heck, I've heard some gear sound appreciably different just by setting the component on a different surface or by using different footers.
On the surface, one would think that performing the evaluation keeping everything exactly the same would be the fairest possible methodology. In my experience I have found that this is not always to be taken for granted.
These days, when I make such comparisons, I try to optimize the installation for each amp (or other component) so that each piece will sound as good as I can possibly tweak it to sound. What works best for Amp A may put amp B at a disadvantage (and vice-versa). So what, on the surface, would appear to be an impartial evaluation or observation, may be (unintentionally) slanted due to factors that simply may not have been considered. Your comments about the 3500 sounding "grainy" or "etched" might be right on the money -- but they could also be telling you that the 3500 does not like the same cabling or footers (or whatever) that work well for the JC-1's.
If you haven't had the amp to play with and tweak over a period of time then you probably have not heard it at its best. Brief shootouts can be misleading. Extended evaluations over time are more reliable indicators.
I don't own either amp you're speaking of, so I have no stake in the outcome one way or the other. But I do like to see things done fairly and competently. For sure, there are a lot of variables to consider.
It's just food for thought...