I have just done this a few weeks ago and had the exact same problem.
Get a good flashlight, a dental mirror and dental pick.
I think you will find with the mirror and the light that the backside you can't see is not seated correctly, causing the boot to sit at an angle.
The dental pick is great for putting under the lip of the boot and sliding the boot over the manifold port.
Hope that helps. Also WD40 is your friend!

Cheers
Glenn