Super glue would be a poor choice as a fret slot filler. It would be messy and hard to control, and it doesn't really build thickness or fill gaps well. Ideally you should use a solid material - styrene plastic works well and is available in appropriate thicknesses from model train hobby shops or online. Or you can use standard wood veneer (which is usually right around 1/40 - 1/42" thick, the same thickness as a typical fret slot). For plastic or wood, you just glue in oversized pieces, then trim/sand flush to the fretboard afterwards.
You don't need to coat your fretboard, especially for something harder like rosewood, unless you use aggressive strings and play aggressively. You can always do the conversion without coating it, and then see how it looks after 6 months of play and decide if you want to coat it then. Coating fretboard on a used bass with unknown history can be hit or miss, if the fretboard was treated in the past (i.e. with those snake oil "fretboard conditioner" type products), it can make coating it a huge mess, since things might not stick well.
As far as a tool to pull the frets, there are lots of choices. You can use standard issue hardware store end nippers - of course, you don't want to actually cut the fretwire, but it's easy to get the jaws of end nippers under a fret to pull it out. Stewmac's fret puller tool is basically modified end nippers, at any rate. When I pull frets, I just use my actual flush cutters - the same ones I use to cut fretwire. Regardless of the tool, the biggest trick is to go slowly and take your time and be mindful of not pulling up chips of fretboard as the tang comes out of the wood. Some frets will just pop right out with a scary-small effort, others need to be coaxed or you may need to try tricks (check the various fretless conversion threads) to get them out without damage to the wood.
Things to be cautious about are well covered in those various threads, too. Probably the biggest gotcha for many people is that once you've removed the frets, you've inherently changed the geometry of the neck, as if you've taken off .04" or so of height. On some basses, you can compensate for that by cutting deeper slots in the nut and dropping the bridge saddles and pickup heights. But, check your bass - if the bridge saddles are already as low as they'll go, or near to it, you might not have enough adjustment range. If that's the case, you may need to shim your neck to bring it back up such that the fretboard is at the height that the frets used to be at.
