What a poor episode!!!
The end of true Red Dwarf?- no, that was when Rimmer left

Asinclair's message from Christmas Day 1998 has been moved to the rumours section in the Starbug Lounge

How could the nanos create a SUBATOMIC Red Dwarf out of atoms?

By breaking down atoms into subatomic particles such as quarks and gluons and so on?

When they were trying to think of famous one-armed people, I kept thinking of a one-armed professional Baseball player named Pete Grey, who took up Golf when he retired from Baseball.

This episode did leave a number of interesting time questions.
In Psirens the crew were woken up after 200 years, chasing after Red Dwarf. Assuming this was a straight line they would be about 202 years away by this episode. Although since Epideme did tell them how to improve their engines by 300%, so if I've done the math correctly, it took them 246 days to get back. (My math is notoriously bad so feel free to double-check.)
Considering the size of the Nanobots they work incredibly fast. If a hole in Lister's underwear is the size of a galaxy, Lister's arm must be the equivalent of billions of light years. And yet now only do the Nanobots quickly rebuild a new arm they also rebuild Red Dwarf which is several miles across.

I believe in Psirens they thought Red Dwarf was stolen by Rogue Simulants.

I wonder if going into deep sleep and flying to this system has really ruined Kochanski's chances of finding a way back to her Dave?

Nobody seemed to suffer the memory loss that occured in Psirens, but maybe it's because they weren't asleep as long.

They must have traveled in a bit circle or the nanobots kept changing direction to shake them off.

Bet part of the episode: Seeing Red Dwarf in the viewscreen and hearing the start of the original theme.

The one where we get the Dwarf back.