I believe the Gen 3 NA ECU and engine loom are different to the Gen 2
Perhaps check with 'toyodiy parts' or JP-Carparts.com to compare the part numbers for stuff like engine mounts and clutch slave stuff to see if they are the same for the early and later models.
Perhaps you could use your old trans speedo drive unit with the new trans to work your mechanical speedo.
Someone on here would know.
Although easy to do, and IMO a great mod for a road car, the later rear X-member swap is an independent suspension mod not really connected to a Gen 3 NA motor swap.
The only parts needed are the later X-member and the longer rear track rods. (And an alignment afterwards)