tldr:
Advanced grinders and mixers: module slots 2 -> 3
Advanced mining drill: speed 3.75 -> 5, module slots 2 -> 3
Gas furnace: speed 2.5 -> 5, energy consumption 50 kW -> 200 kW
Green, Red circuit in laser assembler - crafting speed halved (same as in advanced assembler), bonus productivity +50%
"Air" pipes can transfer other gases (liquids too, but don't do it)
Heat exchanger can heat water with clean steam.

The mod incorporates some compatibility adaptions for several mods to fit in with IR3, most of the implementations are from the IR3 Large Balance Patch mod but without the Balance Patch itself? So not changing IR3 too much and without the hard dependencies. It's not an overhaul. You are good to install or uninstall it at any time in the playthrough and it won't substantially break anything in your factory. Also, you can choose which tweaks you want active. I tried to make everything work and look well in the crafting tab with any mod combinations. For the Mini Trains mod, you can unlock alternative pre-iron recipes for rails and other rail things. Just don't exploit the recycling too much, it still gives you back stock materials...

As for the balance, what bothered me with IR3:
- gas furnaces are really underwhelming, they offer no advantage over the electric ones with 2 eff2 modules, but require a fluid input and an expensive recipe
- proposed solution is to give them at least 1.5x or 2x speed boost like the blast furnaces and possibly about 10% base productivity, maybe at the cost of some energy efficiency
- they will still lose to electric furnaces with T3 modules and beacons late game but at least offer low power draw and more compact builds mid game
-as mining productivity cost is exponential in IR3, getting maximum out of the available resources is substantially important
-I kinda like that most things don't accept productivity modules, but huge basic resource requirements are still limiting for a megabase.
-maybe it's possible to add some researches for recipe productivity of things like smelting like in Space Age? (TODO)
-big chrome drills are fancy, but in fact very weak. They occupy about twice the area as basic electric drills but offer only 50% more speed.
-making them twice the speed of the smaller ones is only enough for a tie, so to compensate I also added a third module slot
-faster laser recipes for circuits feel like a trap. You don't need a lot of them so using direct insertion with basic assemblers seems more important.
-need some other motivation to use them, maybe more productivity? (Made a dirty hack for that)
-geothermal heat exchanger is a rather unique building, but the dirty steam wells are too sparse and weak to use reliably
-it IS a heat exchanger, but can only take in DIRTY steam and nothing more? Doesn't compute to me
-It can heat water for ore washing, which is a good alternative for electric boilers, but finding dirty steam is cumbersome
-you already have clean steam in lots of places, so another alternative could be using solid fueled boilers
-adding a third recipe to the heat exchanger is possible, but requires editing IR3 itself, so I just changed the useless one
-the exchange speed is set so the sum amount of fluids is the same for both (adding a speed mk1 gives you nice 60/s for 1:1 with boilers)
-the air pipes were originally supposed to be a specific pipe type for gases based on the IR3 changelog but the engine doesn't allow it
-I decided to bring back this possibility by removing the fluid restriction on them
-the only advantage of them is a slightly cheaper recipe, so it's supposed to be for esthetic or roleplay mostly
-the buildings using diamond cutters don't offer more than just speed, you just have to unlock them for diamond processing
-I think that's very underwhelming considering the troubles of finding the seed diamonds and setting up diamond refinement
-as a real incentive to switch to them I decided to add a third module slot as well. It also helps with reducing raw ore requirements
-I liked the IR3 Overhaul decision of using water to mine gold as it brings some diversity in mining other than uranium, so you can have that too

The balancing changes are disabled by default though, so you can use this mod only for compatibility. I added my preferred values as defaults for the tweaks, but you can change some to experiment yourself if you like. I may want to add some more changes after enough experience with IR3.

upd 0.0.4: finally got to upload the new version, added some more options, see the changelog