1994 Honda Accord LX sedan, 5 speed, with a H22A swap from a 1997 Prelude. The car started to have a vibration. It currently is setting on 15inch steelies but was aligned for 17inch rims. I am not sure why the car vibrates once it gets above 50mph. Could it be the alignment or possibly an axle? My wife always complains to me saying it didn't start vibrating until I installed the cross slotted rotors. I am not sure about that. Please help.

 

Recheck previous work, verify all fasteners are installed correctly and tight.
Rotate wheels back to front.
If the 15" tires were not properly balanced, it has been a few thousand miles, or if there is water in the tire, these would cause vibrations at higher speeds.
Also if the tires were not balanced dynamically they could be improperly imbalanced. Excessive weights on one side or a tire can be indicative of incorrect balance or a faulty/defective tire.
Alignment should not be affected by wheel sizes, although a larger wheel(rim) and short sidewall may be more sensitive to alignment.
Check that the mating surface of the rotors and the back of the wheel are clean.
Verify the wheels are also not bent/cracked/oblong/bent wheel lip.
Verify the lug nuts are torqued correctly.

 

How were they balanced? Also could be rack/pinion issue or bad bushings in upper joints.. check them all for play.