You're talking two generations of Tacoma. The first generation was 95.5 - 97. The second generation started with the 98 model year.
SR5 is an optional trim package, not a model (as it was sometimes treated in earlier generations). In the mid-'90's SR5 basically included some 'better' trim inside, badging and air conditioning.
The choice of tranny is entirely up to you. Some people recommend autos for really heavy towing, but I don't think a dirt bike makes that big a difference. The manual will be a bit more perky and less subject to auto-specific maintenance woes. If you're talking 4-cylinder, the difference will be more noticeable than in a 6-cylinder.
You didn't specify whether you were thinking in terms of 4X4 or 2WD.