After Effects - Creating Shapes from Vector Layer, not all parts are made into shapes!

Why is this getting so stinkin' complicated?  You could do this in AE Version 4!  No kidding!

• Import the text from illustrator
• Scale it to the desired size
• Precompose it
• Mask the precomp where the split should occur
• Duplicate the precomp
• Invert the mask on the precomp
• Adjust the vertical position on the precomp

You're done!  This isn't brain surgery!

I can see from your screenshots that the shapes are all being converted, but you're running into issues with how they're grouped. As mentioned above, the issue is the way they're built in Ai, which is giving you unpredictable results when converting to shape layers (which I'm not entirely convinced you need to do.)

Confirm if you do indeed need the letters to be separate pieces.
Confirm if you do indeed need those pieces to have full editability in Ae (i.e. whether they need to be shape layers). If not, just import them as separate layers from the Ai file.

There are a lot of tutorials about the Ai to Ae workflow - I'd check some of those out, which will help you with the particulars, but also help you determine how far down this path you actually need to go. This might be a good one to start with.

In addition to what Rick said also check the paths themselves. Slicing up stuff in AI using PAthfinders etc. regualrly produces "bad" paths with stray anchor points that need to be cleaned up. This can have a huge impact on the conversion.

Mylenium

First, fix your Illustrator file by making sure that all of the paths you want to use are on a separate layer and import as a comp. 40 paths on a single layer converted to shape layers will result in a mess of shape layer paths on the same layer which will be difficult if not impossible to animate, group or manage.

Second, determine if converting to shape layers is necessary. There are only two reasons to convert vector layers to shape layers and there are a bunch of reasons not to do it. A vector layer converted to a shape will lose custom gradient fills, styles, effects, some, clipping paths, compound paths, gradient masks, blends and a bunch of other things you can use in Illustrator to class up your illustration. There are only two things to gain by converting a vector image to a shape layer. The first is the ability to animate the vector path vertices, the second is the ability to add shape layer animators like trim paths and repeaters.

Fix you Illustrator artwork first, import as a composition and if you cannot figure out what to do next, get back to us.