Well, here, I'll let you decide if the midis are acceptable.
Toccata:
https://drive.google.com/file/d/0B9s-Ar7XSc3lcjVMUTFQdU9BQU0/edit?usp=sharing
Fugue option A:
https://drive.google.com/file/d/0B9s-Ar7XSc3lTEZiaXVoczh2RnM/edit?usp=sharing
Fugue option B:
https://drive.google.com/file/d/0B9s-Ar7XSc3ldTBNaGhudGtVMHc/edit?usp=sharing
The first Fugue (I think - it's one of the two) is all horns and the second one is mostly horns with some strings. Obviously I don't have to use the same instruments that the original midi had. The only thing I care about (in regards to those 3 midis) is whether the tempo is acceptable to you.
Frankly, I don't like the Toccata at all. Like I said, parts seem unnaturally drawn out (unique to say the least) at 1:15, 1:22 and 1:31 (it is otherwise pretty good with the tempo, I think). I'm not too keen on the mostly-string version of the Fugue, but the all-horn version of the Fugue is pretty good.
If the Toccata meets with your approval and one or both of the Fugues are fine with you as well, I can go ahead and merge the Toccata with one of them and reassign instruments as closely as I can to match the original instrument layout I had before.
If it weren't for those three parts in the Toccata that I specified above, I'd actually like it pretty well. It's tempo is unique but it does have a tempo.
I cannot find ANY other orchestral midis for either the Toccata or the Fugue, or much less both of them together on the same file. :(