As Guy says, do the conversion now. Strip it back while it is in its current state and get the relevant engine mounts and modifications welded in place. There will be a diagonal on the RH side of the engine bay that requires repositioning to accommodate the V6. Then when the car gets painted the chassis and all the mods can be done at the same time.
It will also be much easier to integrate the additional wiring of the Alfa while the car is in this stripped back state.
There are a few guys on here who have done the V6 swap into a Litton chassis over the years so plenty of experience and advice to draw on.
Not sure what what your timeframe for the build is and also what the outcome of the recent proposed changes to the IVA emissions regs are so if it is a long term build then a post 1998 Alfa with a V5 doc would be the safest bet engine wise.

Happy building