My 2000S exhibited the same symptoms as yours. The front motor mount was making clunking noises too. Replaced the motor mount and the shifting was much improved, not always perfect, but the 2nd gear synchro weakness is a known problem with Boxsters. The bad motor mount just aggravates it.
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2000S Ocean Blue Metallic- 116K
3X Water Pump, Clear side markers, Crios Mod, Front engine mount, Flywheel, clutch, RMS, AOS, MAF, serpentine belt, power brake vacuum line, battery, 2X CV boots, Fuel filter, Oil filler tube, 3X ignition switch, 90K service, gas cap, Coolant tank
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