Hi, Chris,
Not sure it will help, but... My DS8 seemed to have forgotten all of his math facts after a year in the local public school where they used everyday math and never (!) did a timed math sheet. He, too, was fine with the thinking of math, but tried to avoid the effort of calculation, and was never fast.
I decided to try Aleks with him, and it turns out he loves quicktables - which is a surprise to me. I had him start with a review of the addition tables and he actually enjoys it. The timer is set for 3 seconds and he has to type in his answers. After reaching certain percentages, he earns a game (of more math facts). They have addition, subtraction, multiplication and division. The program only allows him to work on it for 15 minutes, and it's all he's willing to do (i.e., doesn't like the basic math program - but we'll get to that).
I just mention this b/c you can get a 30 day free trial on Aleks and maybe your son will enjoy the simple review and gain confidence. For my DS, I'm thinking that once the basic math facts are easily and quickly accessible, he won't avoid the rest of it (longer calcuations, having to write them out, etc.).
And another thing which we experienced - the first time DS8 saw one of those full timed worksheets for multiplication (where he's not that sure of his facts), he was intimidated by the size of it. To get him started, we had to break them into chunks - i.e., just do the first column, or just do the ones you really know easily first, etc. I'd think the teacher could probably do this for him - give him five separate pages of only 5-10 problems each rather than one page of 50 - but one at a time. Let him build up his stamina and confidence before he has to attempt one big one. And if he's not nearly finishing, just start him off with a little more than he did last time. I'm sure it's stressful for him to see all the other kids working through the same sheet more quickly. I'd expect he spends time thinking about the fact that he's not good at it rather than just doing it and finding out that in fact he is fine at it. (We get that a lot - too hard, too much, delay, delay, delay - oh, that was easy!)
As for a LD, we did a full eval. and the LD supposedly appears as the difference b/n the IQ and achievement. Whether or not DS has a LD (not clear in our circumstances), a good testing psych should be able to tell you what's going on.
And unrelated but - I'm surprised your son's school gives A's and D's (!) to third graders. No school around here even grades at that age. A D to a third grader? What's the point of that?!!