Ok, got a little bit done today.
I haven't been totally sure what engine I'm going to use yet so I didn't want to mount anything to the lower bypass cover. Having said that I didn't want to have to stop building because of lack of an engine choice. I discovered that I can still get the lower bypass cover out of the jet once the inlets are glued in place. So the first thing I had to do was come up with a temporary method of securing the lower cover. A couple of screws was what I decided on, When I put the bypass cover in place after the jet is finished I will glue it in with some silicone and also glue it to the inlets with some silicone and use the same screws.

Picture 1.
The first thing I had to do was align the lower cover, the rear half is aligned by the rear bulkhead, but the front needs to be centered. To do this I taped a carbon rod to an adjustable T square so I could line up the front point of the bypass.

Picture 2.
Once it was aligned, I drilled 2 small holes through the cover into the wooden bulkheads and secured it with a couple of small screws.

Picture 3 & 4.
After a bunch of test fitting, sanding, tack gluing etc, I was finally ready to glue them in place. I used a product called Everglass, it is a polyester resin with finely chopped fiberglass that has the consistency of bondo. I used this to permanently glue the inlets in place. The only downside to it is it's ugly, but some sanding and paint will cure that. In order to get the inlets to fit to the bypass perfectly I needed to extend the front of them a tiny bit, this could probably have just been done with fiberglass cloth as outlined in the manual, but I used a couple pieces of carbon fiber that I had layed up already. (these are the black pieces in the picture)

Picture 5 & 6.
Once the everglass was dry, I laid a piece of fiberglass cloth over the front joint and over the carbon extension.

Picture 7 & 8.
Then, some filling and sanding on the outside, and a quick coat of primer to see how things are, and the inlets are looking pretty darn nice!!!