your stock vehicle had a computer controlled carburetor connected to a bunch of sensors and pollution controls. Once you removed the stock carb, you effectively prevented any effective control of the engine by the Electronic Control Unit (ECU or computer). Now, anything connected to your ECU can be removed as it no longer is in use (that includes all the vacuum lines except for your feed to the heater, the distributor, the brake booster and your 4wd disconnect). Simply put, the computer (after things warmed up) read the O2 sensor and then varied the air fuel mixture by way of the carb. The computer also controlled spark advance somewhat, as well as a bunch of other pollution items. Read about it here. There are detailed drawings of the stock vacuum line setup on that page.
The suggestion about going back to stock and getting things working, then removing the computer and its associated stuff (nuttering) from the equation, and then installing a new carb, was not that bad of a suggestion. Right now you don't really know if the engine wasn't running right due to needing a proper tune up, or because something in the stock setup was bad. you also may be chasing that stuff while you need to adjust your carb and timing at the same time. It will be quite difficult to figure out which way to go.
In all likelihood the major problem with your stock setup was probably related to leaking vacuum lines and a needed tuneup. Possibly the stepper motor in your carb failed, or the carb just needed a rebuild. As long as your carb didn't require replacement getting it running right would not entail that much effort, but that's only speculation. Several years ago I was in your place and headed the same direction, pulled off the carb and then labored to get it running right with replacement. After several months and untold hours of messing with a weber I removed it and fuel injected the engine. I haven't looked back since. Lots of choices out there for you and you will be able to get lots of suggestions. What you need to do is figure out which direction you want to go and then we can help.