I'm bit confused by your description of the current finish, but if it is flaky, then I suggest you strip the lot off and start again.....I suppose grain filler depends on what finish you are trying to achieve, I havent done many refinishes, but I have never grain filled cos I like the paint to sink into the grain a bit so I can see the lines in the paint.....I have used automotive cellulose rattle cans with great success... not had the bottle to attempt a sunburst yet though! There is a bit of an art to spraying with rattlecans and if you have not used them before it may be better to do one solid colour for your first bash at it. There are sunburst videos on the tube...an example....
https://m.youtube.com/watch?v=bEj4HhDX7cA
Heres my LP jr copy, bare mahogany neck and body, Halfords white primer and Halfords Satin Black....
[URL=http://s260.photobucket.com/user/paulnb57/media/imagejpg2_zpsc71baa2c.jpg.html][IMG]http://i260.photobucket.com/albums/ii21/paulnb57/imagejpg2_zpsc71baa2c.jpg[/IMG][/URL]
Same paint on 51 p bass sprayed last week no primer......
[URL=http://s260.photobucket.com/user/paulnb57/media/image_zpseewhm72o.jpeg.html][IMG]http://i260.photobucket.com/albums/ii21/paulnb57/image_zpseewhm72o.jpeg[/IMG][/URL]