It would be an interesting to see if the TVM could be adjusted to serve as a bridge between the classic and post 2005 series.
There isn't much of a plot other than the regeneration and the Master attempting to steal the Doctor's regenerations (which comes across as almost something the Master comes up with on the spot than part of a larger plan).
The side quest for the atomic clock is pretty uneventful and dull.
It might help to think of an 'ideal' story reworking and then see how the existing footage can be redirected towards it.
The Daleks and The Time Lords are at the cold war stage of what would eventually become the Time War.
Each has been plotting little schemes against each other and hidden their actions behind agents to avoid open hostilities.
The Master has worked with/used the Daleks and the High Council in the past and has a low opinion of both.
I like the idea of the Master working both sides towards his own ends.
The Time Lords make a big deal of 'arresting' the Master and offering him to the Daleks as an olive branch for his past transgressions against their Empire, but secretly have recruited him to give them Time Lord secrets to push them into open war with other races in the hope that they will get rid of the Daleks for them.
The Daleks make a big deal of 'executing' the Master as a representative of their Time Lord enemies but secretly have recruited him to infiltrate Gallifrey by giving him the means to take over the Doctor's body and his Tardis.
In reality the Master has pulled an "Inception" on both of them.
He wants to survive and ultimately get rid of all of them and killing the Doctor and using his heroic reputation to further his goals is just fine by him.
In the new series we have Prisoner Zero, a Multi-form which has a snake body but can take the form of unconscious people.
In the TVM we see the Master take a similar form but to physically enter a human.
In the old series the Master could do this without having to take a snake shape.
The atomic clock is too mundane a quest goal, it would be more interesting if it was a bit of alien technology that has somehow found itself on Earth but linked to time manipulation (maybe a Time War artifact that has fallen back through time, like "The Moment" mentioned in The End Of Time.
We have access to new series elements and also Anthony Ainley in the Destiny Of The Doctors game footage and sound files from the Big Finish audios.
It will take some time for me to iron out how these ideas could fit together into a workable plan but I thought I'd mention them to see if these ideas appeal to you.
I would prefer the Seventh Doctor being shot shielding Chang or one of his friends from gunfire than just opening the door.