I started hearing a knocking noise a month or so back. The mechanic told me that perhaps the sound was from the loose short ram intake/filter.
Yesterday, I reattached and tightened everything but did not disconnect my battery or pull fuses.
You may want to have your motor mounts inspected and replaced if needed; When you rev/accelerate your engine, the entire engine leans forward and back again. It sit on top of four urethane motor-mounts. If they are old/warn, then will allow your engine to move at a greater angle than recommended. Motor mounts cost about $30/$40 for a "kit" of four, but the installation is involved and is advised to be completed by a professional.
http://www.monkeywrenchracing.com/product_info.php?products_id=482This could very-well be the reason why 1) you hear knocking when switching between gears 2) your acceleration isn't as smooth as it once was when your Celica was band new 3) your SRi may have more "play" and is knocking against the radiator fan housing at each engine acceleration / gear shift.