[T-Mobile Samsung Galaxy S II SGH-T989] RealPariah:
Easy to do with Windows based (Linux to) auto patcher. Could also follow directions to do it with device based script.

You should for full effect, but still get some great changes without having to do it if you really don't want to.

Oh that new utility called ApG (Windows gui but has links to that all over ROM patcher for other OS, does pdroid and other add-ons patches too very sweet) also can do service.jar edits for supercharger from downloaded ROM zip in Windows Linux and Mac and that gives you recovery flash zip so can do it auto style before even installing ROM if you wish too try that.

I USE THE WINDOWS PATCHER FOUND IN SUPERCHARGER THREAD THOUGH:

I have my services.jar done in 10 min just use network file explorer to serve my file to my desktop and jump RDP to use my computer to run auto patches. Then copy it back to my device and restart and clear caches and done. Can do it from anywhere as I have RDP accessible from internet :) and it runs nicely over a 4g connection.

Device: T-Mobile Samsung Galaxy S2 [T989 (Hercules)]

ROM: Paranoid Android [2.50 (unofficial)]

Android Version: 4.1.2 (Jellybean)

Supercharged (Nitro Nullified) modded Services.jar and KaK

---------- Post added at 03:25 PM ---------- Previous post was at 03:14 PM ----------

It's the tweaks though and not the kernel that pimp my ROM sounds like way more trouble than it's worth.

I keep forgetting to update my signature but using newest kernel with supercharger v6 tweaks to awesome effect.

With newest paranoid by the way

Device: T-Mobile Samsung Galaxy S2 [T989 (Hercules)]

ROM: Paranoid Android [2.50 (unofficial)]

Android Version: 4.1.2 (Jellybean)

Supercharged (Nitro Nullified) modded Services.jar and KaK

---------- Post added at 03:40 PM ---------- Previous post was at 03:25 PM ----------

Using newest paranoid with newest kernel, been using kernel since paranoid 2.50 though so it's fine to use. I use the unofficial paranoid and he lists the build dates next to download links.

Are you using some set of tweaks or have you tried going in to recovery clearing cache, dalvick cache, and fixing perms yet?

I use the newest TWRP recovery as opposed to CWM, Newest TWRP blows away CWM with its multiple zip flashing, clearing caches option when flashing New zips is done, etc.

Download Goo Manager from market and in settings is option to flash newest open script recovery if you want to check it out easily without needing Odin and a computer.

Of course I also flash kernel using TWRP now also.

Last I highly suggest you download flash zips via Wi-Fi and not mobile data to ensure there is way less chance of errors in transfer.

Device: T-Mobile Samsung Galaxy S2 [T989 (Hercules)]

ROM: Paranoid Android [2.52 (unofficial)]

Kernel: King KANG One .12

Android Version: 4.1.2 (Jellybean)

Supercharged (Nitro Nullified) modded Services.jar and KaK

---------- Post added at 04:10 PM ---------- Previous post was at 03:40 PM ----------

It doesn't necessarily clear all tweaks, some apps like system tuner keep their tweaks and values in a /data/app or sdcard directory to supply when app loads after boot to accommodate ROMs without init.d support, be sure to format system and data to be sure you clear it all then flash your ROM then the kernel then clear cache, dalvick cache and restart.

Things saved to sdcard not applied if app isn't in data to load saved information so don't need to format sdcard. Just be sure to reset any saved data when you reload a tweak app back to defaults before rebooting to be sure something saved that caused an issue wasn't reapplied.

Device: T-Mobile Samsung Galaxy S2 [T989 (Hercules)]

ROM: Paranoid Android [2.52 (unofficial)]

Kernel: King KANG One .12

Android Version: 4.1.2 (Jellybean)

Supercharged (Nitro Nullified) modded Services.jar and KaK