There is almost no difference in a MR-4TC and the MR-4 Rally, just longer shocks and different steering connections and different front and rear bulkheads. The inner body will not fit on the MR-4TC because of how the servo is mounted on the chassis. If you want to convert a tc to a rally you would have to get a rally chassis and about 60 bucks in other parts to get the job done right. I just converted one of my rallies to a MR-4TC special and I found out that the rally is slightly different than the tc.
As to your other questions I haven't seen a YR4 or a MX4 before, but if they use the same tub chassis that the MR4 uses then you could use the dust cover on them.