I can't figure out how you got that speed improvement. The time you save by removing the /i flag is lost when you build a large array in memory (45,000 words in my machine).

Besides, do you really think an all-uppercase output is better?

$ time perl wsearch.pl owijfwapplelaskfiwejfcherryalkfwiofwfblossomowiejf
  1 Al
  2 apple
  3 as
  4 ask
  5 blossom
  6 cherry
  7 err
  8 he
  9 her
 10 Herr
 11 Io
 12 Los
 13 loss
 14 mow
 15 of
 16 so
 17 we
0.30user 0.00system 0:00.30elapsed 99%CPU 

$ time perl wsearch2.pl owijfwapplelaskfiwejfcherryalkfwiofwfblossomowiejf
  1 AL
  2 APPLE
  3 AS
  4 ASK
  5 BLOSSOM
  6 CHERRY
  7 ERR
  8 HE
  9 HER
 10 HERR
 11 IO
 12 LOS
 13 LOSS
 14 MOW
 15 OF
 16 SO
 17 WE
0.48user 0.00system 0:00.48elapsed 99%CPU 

Of course, I ran both scripts at least 4 times, to make sure that the storable file was created and that both scripts were reading their input from the disk cache.