The Redstone Pnematic tubes are for nothing, I originally had a timer hooked up to them with filters pulling out of the machines. (But that didn't work) And what is wrong with using redstone dust? It's just to make sure that the timer pulses the pnematic tube. And it was a 2s timer btw. Do restriction tubes cause more lag than just having nothing? I thought of using the distance thing but just to make sure I used restriction tubes. The void pipe/hopper thing never worked, I have a filter outputting into obsidian pipe then void pipe now. I thought lava caused lag... guess not. And i'll probably put relays on the front of my machines, I want to be able to shove as many items in the ender chest as I want at a time and have them all get processed.
Redstone dust is slower in calculation and causes some overhead if used together with RedPower. With a single block the effect won't be noticeable, but if you build bigger machines and combine both, it will get significant at some point.
What did not work with your filter setup? As this is usually the standard way of pulling things out of machines. The placement of the filter matters though, for example with Macerators you need to place them in front of the machine to pull out the dust. Another idea is to use mangers to pull out the items from the chests (and machines as well if you have the resources to build enough managers). A manager (with no item inside) will automatically empty everything from the inventory it is attached to. This is a lag-free and very fast way to pull items out of an inventory.
Restriction tubes do not cause lag, they are just a logic item, but as far as I can tell from your pictures they do not help on the setup. You should consider a setup of tubes, filters and restriction tubes as a set of: "if it matches filter A -> filter A, else if it matches filter B -> filter B, ..., else if nothing matches -> restriction tube." An item will always take the shortest, possible path and restriction tubes act like they are 1000 blocks long. It is a bit like programming, just with tubes.
Lava does not cause lag by its own, it just causes lag if it flows, but this is the standard Minecraft block-update lag that you get with everything else that changes the world as well. As items get instantly destroyed if they are thrown into lava, this will cause no lag at all. Just be carefull to not burn down your house...
You should not put a relay in front of every machine, as again an item always takes the shortest, possible path. So if you have 4 furnaces each one with its own relay, the items would all go to the first relay, keeping the first furnace busy, while the others will be idle. That is why the relay has to be able to access all input slots of all furnaces (in this example) at the same time, so it distributes the items between them.