They are physically different. The 3550 has a separate bellhousing while the 3650 has an intergrated bellhousing. The 3550 will bolt up to a 5.0 or 4.6 while the 3650 is 4.6 only.
The 3650 is rated at 360 ft-;bs while the base 3550 is 350 ft-;bs.
The later TKO versions of the 3550 are rated at 500 and 600 ft;bs