Well... I'd be pretty good with the outcome your're getting!
Water based top coats don't tend to change the color much, so I don't think it will darken it much. If it were me I would put a couple of coats of dewaxed platina shellac between all of the water based products. Platina doesn't add much color, and it will help with pulling. Brushing tends to pull a bit more than spraying, so I end up using the shellac a lot. What will you be using for top-coat? I have just switched to using BriteTone from Crystalac. Prior to that I used General Finishes High Performance--which I definitely do NOT recommend.
For filler you won't have to worry about the pulling if you use a clear filler like Aqua Coat.* It dried super clear and doesn't yellow--but it's pricey and I have found that it requires quite a few coats to really fill. But it has worked for me on translucent finishes. Crystalac also makes a clear filler, but I have only used the one from Aqua Coat so can't speak from direct experience. You can also tint the filler as TD suggested. I think Famowood filler would work, but you'd need to tint it since it's pretty light color. Timbermate may be OK too, tinted, but I haven't used it myself.
I saw a video of one of the owners of Crystalac using a foam brush, so I know it can be done. His daughter recommend I use an orange Taclon brush, like these:
I have tried a lot of applicators (foam, with and without the brush handle, wipe on rags, sash brushes, goat hair "hake" brushes), but so far the Taclon brushes and a great deal of practice have been working best... My technique, however, is still a work in progress ;-)
*The clear fillers will activate the stain a bit, but it just tints the filler the same color as the stain which you are just working in to the same area...so it hasn't really matter on my builds.