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I think the most likely culprit is a ground loop between the Vox and the TF.
You could try changing the orientation of the TF wall-wart (I mean literally turning it over and plugging it into the wall/extension cord/power-strip upside-down). Not sure if this will help… sometimes it does, sometimes it doesn't, but it's quick, free, and easy, so worth a shot.
There are several isolation boxes on the market… one is the EbTech EB-2, which works well in most applications. Those are around $65 give or take, but there are other alternatives and if it doesn't work, you can return it. The idea is to use a transformer to pass the signal from one device to another without any direct electrical connection (just to avoid any confusion with some "hum eliminators" that are really variations on noise gates or pass filters or other types of EQs – won't fix the problem, just covers it up and your tone right along with it).
The Factors do boost the treble response a bit when not using true bypass, so this may be what you're hearing (if it's more a high-frequency hiss and not a lower-frequency hum). What bypass type are you using? You could try true bypass to see if it helps (I'd miss the tails naturally decaying, but that's just me and certainly not for every song or every player).
Have you tried different cables? Maybe longer cables so you can move the TF father away from the VOX or any power supplies and/or power strips, or maybe rotate the pedal in relation to the VOX (offset by 90 degrees seems to be the best). Maybe different tubes? The tube closest to the input is usually the culprit and might be causing an impedence mis-match, but again, I'm not looking at the VOX schemactic at the moment, so I can't tell you exactly what's going on there.
Also, I don't know the specs of the AC15C1 off the top of my head, but there may be an input impendence mis-match, although that's only a slight possibility. If you have another pedal that you know doesn't produce the hiss, you could try putting it between the TF and the amp. Boss pedals are usually a good choice, although the buffers in the TF are really good, too, and I'd be a little surprised if that's where your hiss is coming from.
The only other thing I can think of is that Vox makes some notoriously "noisy" amplifiers, and always has, but hey, at least they don't burst into flame any more, right?? They're not all noisy and the ones that are seem to only be noisy when they want to be. (But, almost all of them sound really good!) And at least you know you're not the only one dealing with this issue, nor does it seem to be just Vox amps, either. I believe I remember someone having similar problems with a Carvin, maybe a Framus, or maybe a Randall, or maybe I'm just remembering something else.
Anyway, I hope this helps somewhat. Just keep trying different combinations until something reduces the hiss to a level that you can live with, if it doesn't completely go away. Oh, FWIW, my Orange Rocker 30 has always been much quieter than my Vox AC30 Reissue, no matter what I've got plugged into either of them.
Oh, and I agree with you that, in your rig, using GTR/AMP levels is the way to go. Line-Levels might cause more problems than they'd solve, in your setup at least.
Hope you figure something out that works better for you. Definitely keep us posted of your progress! If there's anything more I can do to help you figure this out, just let me know, ok? Good Luck!!