Wow, great thread, just read the whole thing (I know, get a life!). VERY interesting how over the life of the thing, opinions on many aspects are all over the map: great tone-crappy tone, one trick pony-versatile, like-dislike, new built better-old built better, etc. etc. Just goes to show, so much is subjective.
For what it's worth though, through the miracle of modern "research," here's some clarification on various Macca related points. Thanks to Andy Babiuk's book "Beatles Gear" and then the more recent one by Tony Bacon and Gareth Morgan, "Paul McCartney: Playing the Great Beatles Bassline," an entire book devoted to Paul's bass playing and his basses and which one he played on what song. In fact they have a song by song list of every officially released Beatles song and what bass was most likely used (and WHO played it).
Paul didn't "inherit" Stu's bass when he quit (he died later), Stu played one of the big bodied single cutaway Hofners. On p. 49 of Beatles Gear (2nd ed.) there are several different fragments of the story, including two separate and slightly contradictory interviews with Paul himself, then the recollections of the shop salesman, and that of Tony Sheridan and Pete Best. Paul himself doesn't say he got it custom made left-handed, but he doesn't clearly say he bought it that way off the shelf either. He did say he paid 30 British pounds for it. The shop salesman only remembers the installment deal they worked out, but Sheridan insists that there just weren't many decent instruments around, much less left-handed, because there were very few home-grown German rock musicians at that time. So he insists that Paul got it special ordered, as did Pete Best who was supposedly with Paul on the day they first saw it (a right-handed one) in the shop, "He didn't just go into a shop and buy it off the peg, he got it custom made." Author Babiuk surmises that's what probably happened, Paul saw and liked the right-handed one, realized it could easily be converted, and asked to have it done (or have one made that way).
The first Hofner (the block lettered headstock, close spaced pups) was stolen around 68, as someone already noted. But the second one, which he got in late 63, is the one he used almost exclusively from that point on, and is the one he plays today (however maintained/modified/restored/whatever). Rickenbacker gave him that bass in late August 65 when they were in California.
As for the songs, some real surprises. Bacon and Morgan think that he used the Rik on MOST of Rubber Soul, and from then on almost exclusively until the White Album, when the lefty Jazz Bass appeared. So that means...wow, Michelle, Drive My Car, Nowhere Man, Day Tripper, Got to Get You Into...Taxman, all of Pepper (I always swore Little Help from my Friends and Lucy were the Hofner...woody tone, very short sustain), were ALL the Rik.
Whew, sorry for the novel...I get into this stuff! Check out these books though, they're both very informative.