I'm the bloke who did the Matchbox 109E seen on LSP update on the 7th January.
My thoughts on the aftermarket bits available, for what they're worth:
I used a PE set from Eduard for the cockpit, replacing virtually all of the kit parts. I scratchbuilt a few items in there as well, though.
I don't know about resin cockpits as I didn't use one.
Don't get a vacformed canopy - I did and it's designed for the Hasegawa kit, and the rear fuselage is a completely different shape to the Matchbox one, so it won't fit. I used the Matchbox windscreen and rear section, and used the vacformed centre section with a scratchbuilt frame.
I used Quickboost resin exhausts which were great - hollow moulded and with a visible weld seam. I did have to expand the kit exhaust recess to get them to fit, but I was scratchbuilding the front edge of the exhaust shroud anyway from plastic sheet, so that didn't matter to me.
As for decals - the world is your oyster. Have a look on Hannants website and find a scheme you fancy.
Hope that helps,