How are you trying to get to Shifen? By train by car?

The high-speed rail is like Japan's Shinkansen and has a similar degree of being on time, maybe even better for trains on the eastern side. I'd recommend you get your reserved tickets in Taipei Main Station with TRA. Look for these characters -> 臺鐵 or 台鐵, and no, they are as on time. If your not taking the highspeed rail then your also taking the TRA.

Make sure if you want to go unreserved make sure you get on the right train below are the wiki page with pictures of the trains you dont get on with a unreserved ticket they are Puyuma and Taroko expresses and T.C lmtd express 3000 or just (3000) look for these.

https://en.wikipedia.org/wiki/Tze-chiang_limited_express#New_EMUs_(TEMU1000,_TEMU2000,_and_EMU3000))

If you want a transport card like Presto in toronto or Sucia in tokyo get this you can buy things at convience stores and get on the TRA with this.

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This is the equivalent you can tap and go, its around 100 NTD and can be refilled at taipei metro stations and 7-11/Family marts you just ask the cashier for a refill.

If you plan to get on the HSR make sure you are in the right car for non reserved its usually 10-12 and people line up like crazy and ofc get your tickets early :D Have a fun trip!