5 speed swap issues

[STeeL25T]

Hey guys. I finally got my 2005 Saab 9-2X transmission bolted to the motor tonight... However upon doing so I see a few issues.

Firstly, several of the bolt holes do not line up. I currently have it being held on with three.. the two bottom ones that come out of the block and one at the top right (staring at the back of the motor). I might can get a small one in through the lower middle right, but I don't order a bolt for that. I skimmed through both Tom and Hucks (heh) guides but I didnt see any mention of this issue.

The two bolts that go through the starter are also giving me issues. The bottom of the two has no hole on the SVX block, so I cannot get a bolt in there. The top one that has a hole through the block wont work with either bolt I have, but the main issue is the bottom one. Am I the only one having this problem? Or what did you do to solve this?