If you drive daily and arrive at the Lion Rock tunnel before 0730 hrs, you may skip the traffic jam.
I drive daily from Tai Wai to HK for the last 2 years and I dare not use the tunnel after 0730 hrs. I took the Tai Po road and usually it takes about 10 minutes from Tai Wai KCR to Garden Bakery in Sham Shui Po. However I don't know how long it will take from Garden Bakery to Pak Yu (via Tai Po road, Nathan Road and Shantung Street etc.)