I have a Sigma 50mm f/2.8 Macro which I have used a lot, mostly used for fairly static subjects - it's as cheap as they come but it is among my sharpest lenses. However, I too feel that a longer lens is preferable, and about 100mm seems like a good choice. I realise the Nikkor 105mm VR is rather expensive, but it is supposed to be really excellent and may hold its value better than some of the others (particularly if you buy used to begin with). Nikon make an 85mm DX VR which is much cheaper, not so well regarded, but really there is no such thing as a really bad prime macro lens.
You could possibly try your 55-300 with an electronically coupled extension tube. I would imagine the viewfinder would end up quite dark and AF might not work either, but extension tubes are useful things to have anyhow.
Depending on how much detail you want you could try a close up lens on the front of the 18-55 at 55mm. Generally you don't have to get quite so close as you would with the same lens and extension tubes, but the quality is a bit or a lot worse. I have one made by Opteka around somewhere - the quality doesn't get close to the dedicated Macro lens but it's pretty fun and cheap.
I tend to shoot macro photographs hand held, but this is not normal, indeed, it is a challenge, but I like walking around and finding things. I also find it difficult to keep a moving (windblown) subject in focus when a camera is on a static tripod. If you are taking this seriously a macro focusing rail might be worth investigating - do you have a sturdy tripod already?
I'm not sure I would use flash for eye photography. I think good results should be possible with a bright window and careful working. If you do want to use flash, you could do what I do (for cheapness) which is mount manually adjustable speedlites on stands and use cheap wireless triggers. I guess you could mount your sb400 off camera with an appropriate cord and keep the metering.
