Kelly,
A big Type 1 is a finicky beast for a variety of reasons. I think you are experiencing the results of several of them. If I understand you correctly-- you catch glimpses of what you think the car is capable of, but are too often left wanting.
I have no idea who built your engine or what heads and cam it's got, but what we know about what is bolted on seems to be at least as important as what we don't know about what's inside (at least as far as it pertains to your complaints).
If this were mine, I'd start with the known problem (you have a lot of spark scatter), and only go forward after that is resolved. I've had nothing but bad luck with Pertonix modules, and would change that out before doing anything else. I've not had a bunch of bad luck with the 009 copies-- but I never tried super hard to make one work, as they are known to be suspect. It seems like you agree, when you say:
Not averse to trying, but have no clear advice on how to proceed. Magnaspark?? I'd do that too, need to study up on what to buy. Any CLEAR recommendations for what to buy and where to do so would be much appreciated.
I would submit that several people with personal experience have recommended the Magnaspark distributor from CB Performance very clearly and specifically. It's $226, and comes as a kit with a nice coil and wires. There's nothing to program (like crank-fire or the CB Black Box), and swapping a distributor is about as easy a task as you're going to find. This one is "plug and play". You'll need a timing light, but it sounds like you have one.
Once you have the spark sorted, I'd turn to fuel. As many problems as you've experienced, I'd start at the beginning.
I wouldn't start with the carburetors-- I'd start with the intake manifolds. If you've never had them off, I can almost guarantee you've got a vacuum leak at the intake manifold/head junction on one or both heads. There's a lot of weight cantilevered out on two little studs, and they tend to loosen up with the vibration and heat/cool cycles. Couple that with how difficult ported heads are on intake gaskets, and I'd bet you are leaking between the runners, or to atmosphere, or both. This is advice born of experience-- if your engine has ever backfired, they're leaking.
Fixing that means being a contortionist. you'll need to take the entire intake system off, then remove the manifolds. The gasket will stick to the heads, almost assuredly. You'll have to stuff rags into the intake ports to keep crap from falling into them, and then carefully scrape the gaskets from the heads. You may need to remove a rear wheel and some of the surround tin to do this. It's not easy.
Once clean, you'll probably have to make or modify your own intake gaskets, because the heads are likely ported, so the intake runner holes in stock ones will be too small. You'll probably want to make sure the intake manifold flanges are flat as well. Most guys lay a piece of sandpaper face up on a piece of glass, and move the manifold across it in a figure 8. You're out of luck on the head side, beyond making sure it's clean. I coat my gaskets with Never-Seize for the next time I have to do it. I also use special shouldered intake nuts that take a 10 mm socket on the studs. These are not hardware that can be purchased at Ace or Fastenal (they come from VW specific places. I got mine from a guy on TheSamba). These nuts from Gene Berg are something I'd like to try-- 10 mm hex head, peened to be lock-nuts (without plastic inserts)
Only then would I turn to the top of the intake, and start worrying about the carbs.
It seems like you've got a good set of carbs, but you don't trust them. I know it runs counter to your way of doing things-- but honestly, if I had as many issues as you, I'd send my carbs out to a "carb whisperer". Everybody used to talk about Art Thraen as the go-to carb guy. I sent many sets out to him. I stayed in his house a few times. Art is my friend. Here is a secret-- Art didn't do carbs himself since about 2000 or so, maybe longer ago. He trained a guy who worked for him to be the carb guy, and Dave (the guy) has been doing them every day for many, many years. Art sold the shop to Justin McCallister, but Dave is still there. The shop is called Blackline Racing, and they do fantastic work.
... but they aren't doing anything that Danny hasn't offered to you. I'm 100% sure that if you sent Danny your carbs, he'd go through them with a fine-tooth comb, rebuild them, set them up correctly, bolt them to an engine (probably his), set the mixture screws and air-bleeds, and get them back to you in a trustworthy state. After that, you'd still need to set your linkage up correctly, but that's something Cory can help you with in his driveway.
That's my advice. I'd either do all of it, or none of it. The "shotgun and hope" approach has not served you well so far, and I sense you'd like to be done with this for a while. This is a way you can get it running as well as possible.