What's not to like?!! I think those side covers look the dog's bollocks - bit cafe but a bit more modern wrenchmonkees vibe.
And the seat - what's not to like?
I mean what's not to like - total? Probably my favourite bike on here.
Thank god it's not another crappity smacking bobber. You've inspired me anyway.
Top job.
Go take a victory lap I say  

I agree that the bike is sweet looking......and the seat is not quite keeping up with the rest of it.

I think the back needs something to break up the lines - like the Cafe Racer seats have.  I know you want to be able to ride two so you can take your son......maybe you can make a second seat for solo rides that has a bump - even if it is part of the seat padding.

I like the side cover design.  It's funny how sometimes little things on a bike can take a lot of time and work to make.  

Here's a suggestion for future similar projects.  Check out kydex or other thermoformable plastics.  They come in different colors, sheens, designs.  If that sweet bike were mine I'd see if I could find ways to use them to make covers, housings, etc. Durable, light weight, easy to use, shape, reshape, drill, no rusting.  The use is endless.  Now, your bike has an old school appeal to me and so you might want to keep everything metal for that purpose.  But I guess I'm trying to open a window of imagination and possibilities that are clear in my mind but kind of hard to convey in this early morning hour.  Here are some unrelated to motorcycle pics of stuff people made that might help see how DIY thermoformable plastics could possibly be used in bike mods.    
http://www.parallaxtactical.com/store/bmz_cache/c/c1930c1d1354b8cf8e616088840...
http://gr8holster.com/assets/images/autogen/a_Kydex_molding.jpg
http://www.teamcrc.com/store/images/products/1357.jpg
http://i.ebayimg.com/t/TOPS-Fire-Starter-Piggy-Back-3-Rods-Magnesium-Ferrociu...

Here's a vid of a guy who made a simple DIY vacuum forming setup using stuff from a hardware store and a shop vac.  I'd love to figure out how to do this with headlight housings, speedo housings, etc.


http://www.youtube.com/watch?v=50-sR54UBgY 

Maybe there's a way you can make a seat pan shaped like you want then cover.  Or maybe the back section could be a faux raised area but still be coveed to look like the one in the previous post with the red stripe. Or maybe a similar profile but the rear is a storage area.

Is it the look or the feel of the seat that you don't like?  It looks very much like the seat on the Triumph Bonneville T100.  You might try doing something like the Thruxton:  it uses a standard flat 2 person seat, but it has a fairing covering the aft portion of the seat for that sporty look.  It pops off easy, so it's cafe when you want and 2-up when you don't.