It seems that your main concern is whether we should question the Canon because it might not be perfectly transmitted. I think that putting aside the transmission issue one should still question the Canon since the Buddha taught that one should not accept what the Buddha teaches just because the Buddha teaches it.....he taught that one should find out for oneself if his teachings work or not....and for some this process of finding out involves alot of questioning.
Also, it doesn't matter if the Canon is perfectly transmitted or not if it works....and in my experience it does work....even if you don't accept some of it but merely withold judgement on the parts which seem unlikely in your view.
Thank you, chownah, in essence I agree but I have a couple of caveats. One is that you have only this life in which to test (if you have another life following, it will be a "clean reboot" and you won't have the information garnered in this life). You cannot, therefore, say if this understanding of the dhamma gets you to insight more quickly than that understanding of the dhamma. You can see progress, but can't know until you reach liberation (or don't) whether it's progress that will get you liberated or not. So while I agree with you -- and with Ben who says that practice is the ultimate test -- in a sense it can only be a really good test of what is not the dhamma, that is, we can most easily discard what does not work.
My other caveat is that I believe that what the Buddha taught has more internal consistency and coherency than any other system I have ever seen. This being the case, it is helpful to put together a good understanding of what he taught, just because he taught it. On the other hand, of course, he did not have our more advanced science and technology to (for example) see exactly how the mind works and the senses work, being two different systems, one "over" the other, so there you are quite right that just because the Buddha taught it doesn't make it so.