Uppercase, I've just pretty much done the same with my JBA-4 kit.
http://www.buildyourownguitar.com.au...ead.php?t=3985
Not sure if you have purchased the kit but from memory there is now a fret-less 5 string version in the PBG shop, could save some time?
To remove the frets I used an old fashioned butter knife. I just slipped under the end side of the fret, lifted and pulled out by hand.
To fill the frets I used superglue and maple saw dust. It worked but was a real pain to do especially along the edges. I recommend veneer (you should find something on YouTube on this...). Others in this forum have mentioned cable ties, plastic plant pot labels so other alternatives worth exploring
Finishing the fretboard - I believe a good finish is required else the strings (especially roundwound) will make a mess of it with no frets to push against. I use flatwounds over a superglue fretboard and no damage to date. I used superglue on my fretboard but would use epoxy in future (as forum member Wazkelly also recently mentioned in his fretless bass conversion). Superglue was a bit of a pain to get right due to clouding issues but with persistence came up well.
For the nut I lowered by sanding from the bottom (its a flat-bottomed style nut and not radiused on the underside like a Flunder JB). The nut on mine is very low.
Hope that helps!