First you have gone to extremes on trying to correct this. The TPS setting on my 07 corrected poor low end throttle response and eliminated the 2000 to 3000 RPM poor torque .I need to do some digging to find that setting, it is definitely higher than factory.Second thing is Invader posted the vacuum hose mod, using 6 inches of vacuum line. Have you done a throttle body sync?
As to your coils, the 07 and 08 were known to crack, you should have a close up look at the area just above the plugs, look for fine lines of tracking. Second thing is when inserting the stick coils, sue a good dielectric grease , on the outside sealing boot and a small amount on the rubber boot that goes over the plug. One word of caution, everything needs to be clean and dry, if it isn't clean tracking can occur, just remember a spark is hotter than the surface of the Sun.
For what you have invested I would replace the stick coils, again Invader had posted several good replacements.I would also be checking all my vacuum lines/ replacing them.Is your airbox mounted properly and tight? Have you checked your wiring harness just back of the stick coil wiring, this is a known problem on the MK-1 and MK-2. I may have covered some things you have already done, just didn't have a second browser open.
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