Indeed, there are two different "punishing" mechanics at play in TC4 in 1.7.10.
Warp, not flux, is gained from both researching forbidden knowledge and from crafting forbidden items. Flesh golems are good if you want a lot of it, as they can be melted back down into all the aspects necessary to craft a new one- you just need another flesh block. Eating zombie brains is also a popular method.
If you have warp, you will occasionally get warp headaches. The edges of your screen will darken briefly, you'll hear a heartbeat sound, something will be printed to the chatbox, and maybe something else will happen. Earlygame, it's mostly paranoia messages ("Something is behind you..." even when there's not) and the occasional free research point. With more warp, you'll get more serious effects, such as debuffs or enemies actually spawning in.
If you go for a while without gaining any more warp, the time between events will gradually increase, until it stops happening altogether. However, if you do so much as a single forbidden research, the slowdown thing will reset, so you'll get warp events pretty frequently for a while.
In addition, there are two ways to mitigate the effects of warp. Purifying bath salts will give you a buff that prevents warp events entirely. The more warp you have, the less time this lasts; but with moderate warp it'll last about twenty minutes. Sanitizing soap, on the other hand, will remove warp from you, reducing the intensity of warp events. It works better if you use it while under the effects of the bath salts.
There are three kinds of warp: Temporary, "sticky", and permanent. Temporary warp can come from crafting and eating zombie brains, will gradually decay on its own, and is removed entirely whenever you use a bar of soap. Sticky warp (just called Warp ingame) comes from crafting and researching forbidden items. It will not decay on its own and can only be removed bit by bit by the soap- using soap with the bath salts warp ward buff will have a much better chance of removing some sticky warp. Finally, permanent warp is only gained from the more taboo forbidden researches. There's no way to get rid of it.
The Eldritch tab in the thaumonomicon and the Eldritch Revelation research within both require you to have warp. I'm not entirely clear on the requirements, but I think that the tab will unlock once you've got enough permanent+sticky warp, and the revelation research when you get a warp event after researching all its prerequisites. Craft a sanity checker when you can (it's in the eldritch tab); it'll tell you how much warp you have. You'll never need your sticky warp to go very far past the lower marking.
With all that done, Flux is much simpler. Whenever an aspect in a crucible evaporates or overflows, it has a chance of creating a cloud of flux gas or a puddle of flux goo, which will eventually evaporate into flux gas as well. If you leave too much flux goo or gas sitting around for too long, it will start spawning tainted fibers and turning the local biome to Tainted Lands. You can clear it up by displacing it with a block, or with the use of the Flux Scrubber, a more late-game item. There's also a couple other things that can produce flux, such as one of the warp debuffs, but that's the gist of it.
As for nodes... if you get two of them close enough together (the radius is four or five blocks, if I remember correctly), they will start to bully each other. They'll drain and occasionally steal aspects from each other, with the net result that one gets bigger while the other is drained into nothingness. There's really no point in doing this unless you want to create a large node to energize- if you're just recharging wands, having multiple smaller nodes is much more efficient.
You can mitigate the effects of bullying by using Node Stabilizers. The basic one will prevent the node from interacting with other nodes entirely; while the advanced one will only allow it to drain other nodes, and not the other way around. They also reduce the rate at which your nodes recharge, but that can be mitigated by packing in more nodes.
