OK, not sure exactly what youre looking for here, as the sheet music doesnt match anything on the wmv's as far as I can tell.
I have transcribed the wmv's for you, assuming thats what you were after.
First thing to think about when transcribing is work out the beat. Put it on loop and tap your foot to it. Make a note of which note the beats fall on. That will give you your tempo and bar length.
Ordinarily that will get you most of the way there. With this track I could tell immediately it was essentially a 12 bar blues, therefore there was a good chance it was in swing/triplet-feel. You could write it exactly the same as Ive done without the triplet feel and it wont be quite the same, which could explain why you feel you have to lengthen bars, change the tempo and have very odd 16th notes etc. to make it sound correct.
If youre going to copy this you need to set the "triplet feel" button to "triplet 16ths"
I only did the main bit. For the int5erlude chugga chugga bits stick to the same rhythm as Ive used and use your foot to tap out which bits to rest and hold etc. If you have difficulties, I can run it up on GP for you, but it will probably do you good to learn it yourself.
Hope this helps. If not, and you want something done with the guitar pro file you posted let me know.