If memory serves, the TRD mounts are stiffer than stock, so anything causing vibration in the first place would be exaggerated by the stiffer mounts.
My money is your flywheel, they are dual mass jobbies, and would imagine they cause vibration when buggered, the vibration was probably there before you replaced all the mounts, but your stiff mounts are making it transmit to the rest of the car so you can feel it.
I take it you mean vibration at 1800rpm when the car is stationary. If this is the case, it's almost certainly the flywheel, as its the only big rotating mass big enough to cause vibration from the gearbox area.