Thats by design. The replacements are inline and look like that for the automated installer. Just follow exactly and you should be cool.
Your printthread sounds freaky. The original thread should also NOT contain a printthread.php file (i just double checked and couldnt find it!). Im guessing that the one youre looking at is your own that has been modified in gas/changes.
Dont know what you mean for step 207 w/o looking at it again... but most likely its a conflict with another mack or something. I tested the latest install on clean 3.08's and got 0 errors. Regardless I hope everythings cool.
mhme... Looks like you will have to do the changes manually. That is the first time out of hundreds of installs that I have heard that though. Bummer as there are quite a few manual changes with this version