I doubt if the e39 thermostat/waterpump is much different than the e34 in terms of design or reliability. Many people replace them at 50-60,000 miles to be on the safe side. Also, how long has it been since the coolant has been changed? This could be an issue. IMO, use only BMW blue coolant. Just a consideration.
Thanks,
1995 525i Auto, M50TU 2.5L, EAT chip, 1/95 build, USA, 205/65/15 tires, ASC+T, HID, lumbar, EC Mirror, BMW Alpine 5 radio with BMW-Pioneer CD Changer, abt 236k miles, Oxford Green/Parchment