I strongly considered the Beams 3S-GE/6MT swap from an Altezza before I had to part with my '95 M-edition project.
Coming from a mostly Supra/MR2 background, I'm a huge fan of Toyota engines - but swapping the 3S-GE Beams blacktop and 6-spd fron an SXE10 Altezza is going to be far from a walk in the park.
The Beams 3S-GE is a little bit taller than most 4 cylinders, and the Beams 3SGE's from Altezzas were all front sump, which means that you'll be doing a rear sump conversion at the very least, and having seen the engine next to a Miata BP 1.8L I'm not sure that it could be made to fully clear the hood without crazy tweaking such as shimming the front subframe, etc.
Parts are also a problem - other S-series engine parts from US market 5S-FE's, 3S-GTE's, etc generally won't fit the Beams motor.
When considering a 3S-GE swap, make sure it includes the MAFS, ignitor, drive shaft (or at least a cutoff stub for the output shaft yoke off the transmission itself), wiring harness, and ECU. Locating any of those parts separately is a nightmare and very expensive. Expect to pay at least $2k for a decent one, the cheaper engine sets almost invariably have missing parts or other issues.
Best of luck on your build, regardless of what you decide to swap in!