Seems like a lot of little problems stacking up ... 11.65 indicates the battery is substantially discharged. The original generator doesn't do much at idle anyway, so you should recheck at higher rpm (or just have a look at the ammeter). You should see the battery voltage come up substantially at 2000 rpm, and roughly 20 amps of charge on the ammeter. If so, then you need to drive more highway miles (or charge the battery overnight). A fully charged battery should read more like 12.6 with the engine off, and the generator should bring it up to around 14 with the engine at a fast idle.
The supply to the flasher is only daisy-chained at the voltage stabilizer, it doesn't actually go through the VS. So you are losing a full volt in the wiring from the fuse block to the flasher, which is way more than it should be. Probably several marginal connections. I'd probably start with the ones at the fuse block : shine up the blades with a mild abrasive (like a Scotch-Brite pad or a pencil eraser). If any of the connectors were easy to pull off, try crushing the connector just a bit to tighten it up. Smear a little silicone grease (or Vaseline will work) on the blades before you reassemble, to help prevent future corrosion. Repeat the treatment for the fuse & the clips that hold it. If the drop is still more than a few tenths (I try for 0.1, which is usually achievable), repeat the treatment at the VS connections.
My diagram also shows a 4-way union, which I'm guessing is a bullet connector. Might be worth just replacing the sleeve, they aren't too expensive and I've wasted more time troubleshooting than I care to remember, because one of mine was broken internally. The bullets can be polished and smeared; the sleeve can be cleaned with a small wire brush.
11v at the fuse block but 11.65 at the battery means you're losing 0.6 in the wiring and ignition switch. A little on the high side, but that alone won't cause a problem. Still wouldn't hurt to clean up the connections. I found that the TR4 ignition switch (on my TR3A) wasn't making good contact internally, so I ground off the rivet heads with a Dremel, and opened it up to clean and lubricate. For reassembly, I just used some small (8-32 maybe) bolts & nuts.
https://s258.photobucket.com/albums/hh260...metershunt1.jpg