Hardly crazy. That SF was probably the best old-school GC tennis anyone has played in the last 25-ish years (emphasis on "old-school"), and Rafter was one of the few S&Vers who had the skills and athleticism to still make it work today.
Let's get one thing out of the way first: Pat would at least be able to hold his own on serve. Of course the received wisdom says that Novak with the power of his current racquet would be passing him left and right, but if you pay half as much attention as I do to net stats you already know that net rushing is still not only doable but preferable even against the best returners/passers, and while Djoko might be able to reproduce Agassi's proven kryptonite vs. S&Vers on return Dre had clearly superior passing shots and Nole would be hard-pressed to pass Pat better than Dre did in that cracking 5-setter in '01.
Plus Pat's mastery of the underutilized body serve would be unlike anything Novak has been exposed to in his career and that variety would give the five-time Wimbledon champ plenty of headaches even on today's grass. There's a reason why Rafter despite not being an ace dispenser made the top 10 in % of service games won every year from '94-'01 except '95 (yes, even before he won his 1st major), ranking 2nd on all surfaces in '00 with 87.8%, or why none other than Sampras admitted in his book that he preferred to play Stefan to Pat due to the Aussie daredevil's said ability to constantly keep him guessing.
The real Q, then, is how Pat would handle Novak's own underappreciated serve. Now I should point out that whatever improvement we tend to attribute to Novak's serve is less reality than perception as
his # of aces per service game has held fairly steady between his best years unlike Fed's which saw a noticeable uptick from '06 to '08 ('07 stands somewhere in the middle at 0.62), but as expected the #s do show that Novak had fixed his Martinified serve by '11 (0.30). So what was his hold % that year? 90.6% (Wimby was the only GC event he played in '11), which actually is somewhat underwhelming compared to Pat's 91.6% in '00 which itself would likely be at least a point higher today, but considering that Novak had to go through Anderson, Tsonga and Rafa we can safely assume Pat would be dealing with a top-notch service game nonetheless.
So what was his RGW% on grass in '00? 23.2% overall or 23.1% at SW19, which is more than decent on the unpredictable grass of yore (its last edition in fact!) but nothing compared to Novak's predictably dominant 31.3% in '11 which also dwarfs Agassi's subpar (for him) 25.4% in '00. (FYI Pat won 57.7% of his overall games at '00 Wimby and Novak 61.7% at the '11 edition, TBs included.) That said prime Sampras was well-nigh unbreakable in Wimby finals,
holding serve a stunning 127 times out of a total 131 (Pat as expected failed to break him once), and while Pete was playing with tendinitis and a back injury in '00 it's still hard to see him getting broken nearly 5 out of 16 times (or even losing in 16 service games) like Rafa in the '11 final. Not to mention that this isn't a fair comparison to begin with as even the very best passers struggle to pass his opponents more than half the time and Pete wasn't the only opponent Pat faced who attacked the net more often the average player of today. This isn't to say Djoko still wouldn't be ahead of Rafter on return. He would, just not quite by the level of margin suggested by the 31.3%-23.1% difference.
Having said all that, I almost always give actual champs the benefit of the doubt and I do think Novak takes this in a hard-fought 5-setter. Thanks to that RoS advantage of his, yes, but also because the justly lauded Rafter kicker wouldn't have as much bite on grass as on the high(er)-bouncing HCs. I still think Pat would have a slight edge on serve and have his way at the net, but not enough to override those two major factors as his dinks and slices which worked so well against Agassi wouldn't be as effective vs. Novak's superior mobility.
Speaking of which you know where I think Pat would have a better chance? At the USO of course, where his kicker would likely earn him more free/easy points to put him over the hump. And in '98 he was having the run of his life, completing the Canada-Cincy-USO triple and knocking out a feisty Sampras (albeit slightly injured, yes) in the SF and dispatching Flipper in the final while committing only 5 UFEs in 4 sets. That Rafter may well be the fave over '11 Novak, who despite his sterling HC credentials has been underwhelming in Flushing Meadows by his standards. At the very least it should be a competitive matchup.