[b]I didn't use the rubber pads provided by Thermalright, as the shim I was using only had cutouts for the standard cpu pads, and I thought the shim would do a similar job (protecting the core)
Those rubber pads are there for a reason and a shim will not do their job. It's likely that the heatsink is not sitting flush on the core.
[b]... was to plugin the directly to the mobo cpu fan header.
This will drop the available voltage for the mobo and likely cause damage/instability to the mobo itself and the headers should only be used to monitor fans, not power them.