There is a Weapon R header which replaces the cat. The headers for the R18 are a pointless affair because there is only one exhaust port. You just need a downpipe from the head to the catback.
No idea about port/polishing.
I've been researching a lot about engine swaps. Our cars are the FD1 JDM chassis. The FD2 chassis is similar except for : spot welded to reduce flex and a slightly wider front fender, brembo brakes on the Type-R and revised suspension. It comes with two engines better than the the R18 - the K20Z2 which produces 155BHP and the Type R monster, the K20A which makes an astonishing 225BHP. The latter requires 100RON fuel, so it is a no go here. The former will make only about 10BHP more than our R18s when tuned to Indian fuel, which is pretty useless.
Therefore, the only real option is the K24 series. There's quite a few to choose from, the best being the K24A2 from the Acura TSX to the least powerful, the K24A8 from the USDM Accord, which is also released in India. There is also the option of using the 2.4L CR-V engine. There are also frankenstein swaps, which utilize a K24 block with a high flowing K20 head with complete 3 lobed VTEC. The Accord engine for example, is castrated with only the economy VTEC system. However, putting a proper head on the Accord block has its own challenges as the pistons will need changing. But not all K24 blocks have problems with it. Most can accept a proper head simply bolted on. A proper K24 swap will net you more than 250BHP, naturally aspirated, on normal pump fuel available here. You can change the pistons to allow forced induction (lower compression ratio) if you wish and make around 400BHP with the stock internals (no sleeves, no forged pistons/crank etc etc) with 95 AKI petrol. I'm guessing 350 with our fuel. Standard issues with engine swaps apply - if you get a used engine straight from an engine parts shop, it will be cheap, but it will require rebuilding. If you get a crate engine from a tuner shop abroad, it will be expensive.
You'll need a CR-V mount to let the engine sit flush in the engine compartment. You'll need to reroute the A/C lines. You'll need to figure out which gearbox works with your engine. There's quite a few to choose from depending on which block you go with and which year said block is. You'll probably need to change some of the ancillaries like the oil pump. You'll need different belts.
However, with the engine comes a bigger problem. The ECU. You'll need an aftermarket ECU to run frankenstein swaps. The easiest choice is k-PRO, by Hondata. They modify the stock ECU to let you have a fully tunable ECU. However, they do not support 2006+ Civics in any market. The problem is that 2006+ Civics, be it JDM/USDM/EUDM, all have the fancy dash. These dashes use the CAN bus to run the dash instead of plain ole' analog stuff. So everything on the dash is run by the ECU. When you put the nice K24 engine in with the K24 ECU, k-PROed or not, your dash will no longer work. The only choice right now is to run an aftermarket dash like the Pi Xsport.
The other choice is standalone systems like AEM and such. But making them work with the complicated i-VTEC system and the other electronics in the car is complicated to say the least and excruciatingly painful to say a little more. You'll lose airbags, A/C etc etc. Even pros like Bobby Jayaram had enough trouble getting just the FIC to work on their turbo R18 setup.
I know the CAN bus and I've worked with micro controllers in the past using that bus. If I end up doing it, I'll make a board myself that will run the dash with the K24 ECU. Or, if we are lucky, Hondata will come out with a k-PRO which works with 2006+ ECUs. There are some other solutions which make both ECUs work in tandem, with the k-PRO running the engine and the original ECU running the electronics. That is another can of worms though.
In short, you'll need a fantastic engineer who knows his stuff and has a tuning shop with all the bells and whistles, contacts to import the parts (if you are using the Accord engine, you can avoid the hassles of importing the full engine), a tuner who can dance with a k-PRO (you may have to fly him down), lots and lots of money (USD 10K for the hardware, at a minimum), a lot of patience, and a spare car.
Is it worth it? Well, I'd love to have 250BHP in my car.
PM me if you want to know some starting points if you are going for this.