To get a 2D model, open the geometry in SpaceClaim. Use the Move tool to move all the solids/components so that the axis of symmetry lies along the Y axis. Create two planes: XY and YZ. Use Split Body to cut all solids with the two planes. Hide or delete 3/4 of the pieces, leaving 1/4 that have a face in the +XY plane. Select all faces in the +XY plane, type Ctrl-C, Ctrl-V and you will have all the surfaces you need to make the 2D model. Delete all the solids. Go to the Workbench tab and click the Share button.
In Workbench, create a new Transient Thermal model. Don't try to reuse the 3D model you have. On the Geometry cell, open the Properties panel and on the Analysis Type, set it to 2D.
In Mechanical, click on Geometry and set the 2D type to Axisymmetric, then apply all your BCs.
Regarding Time Stepping, have you tried setting Auto Time Stepping to On? That way you allow the solver to choose whether it needs a small time step and allow it to use a large time step. That will save some wait time for either a 3D or 2D model to finish the computation.