We sanded down and stained our hardwood floors for what is probably the last time. We then put down a coat of bona sealer, and 3 coats of bona mega (satin).

Once the floor was cured and we started walking on it, it didn't take too long before we started seeing white lines (white line syndrom, we believe?). We noticed it appeared mostly around boards that were a bit looser / had some give to them. So I put some nails down through the worst offenders. We then sanded/scuffed up the the whole and added another coat of Bona Traffic (satin). For those of you counting, that's 4 coats of varnish and 1 sealer so far.

After waiting a week to let it fully cure, we started walking on it again. Most of the white-lines are gone, at least for now; however, we really did a bad job with the top coat of the varnish. There are spots we completely missed and spots with brush-strokes. I'm tempted to scuff the floor again and put down ANOTHER layer of Bona Traffic.

Is that too many layers? Any suggestions for preventing white-line syndrome - or was nailing those boards the best I can do?

You're fine with waterbase but are starting to push your linits.

the problem with overbuild is susceptibility to marring and scratching.

this is usually around 4 coats oil and 5-6 water.

in these multi application 2 coats of sealer is more often applied plus 2-3 topcoats.

the errors in your last coating almost sound like issues that arise when the last coat hasn't dried sufficiently