Mark,
Not sure what you've got going on there but you can't leave the engine mounts that way. Whatever is amiss probably explains why you had so much difficulty getting it into place. Maybe some additional photos would help us see what is causing the issues with the poor fit.

Although it doesn't matter at this time just as an FYI you have the driver's side pipe on the passenger side in your mock up photo.

Keep us updated and good luck moving forward!

Jeff