Depends on your budget. Many people swear by fremuff (along Sergio Osmena Highway, Makati). Mufflerland can do high quality work, too (T.Morato, Quezon City).

Both Brodeth and eRL can do custom headers of high quality, but you've got to be willing to spend 15-20k pesos.

Other engine mods... you'll have to ask around at places like grupotoyota... I'm not familiar with the 3SFE engine.