Sure, you can upgrade the output transformer. The Magnequest TL-404 will work in the Mainline circuit but you'll lose the balanced output. The Sowter 8983 would also function similarly but also without balanced output.
The V-caps are directional in a certain sense, but not at the signal levels seen in the Mainline. The short leads on those caps should go to the plate of the 6C45 and the long leads to the output transformers.
Yes, you can put a single stereo pot into the Mainline. If you do that, you should take off all the hardware on the front panel and pull the labeled overlay panel off and throw it away since it's no longer correct for the kit. The stereo pot will definitely not perform to the level that the stepped attenuators do, and you will nuke the resale value of your Mainline by doing this.