What are the FAA requirements for an aircraft to be IFR certified?
As you say, the FAA certifies an aircraft for certain "kinds of operation".  For a normal category airplane certified under 14 CFR 23, it basically says that it must be "established appropriate to the installed equipment":


  §23.1525   Kinds of operation.
  The kinds of operation authorized (e.g. VFR, IFR, day or night) and the meteorological conditions (e.g.
  icing) to which the operation of the airplane is limited or from which
  it is prohibited, must be established appropriate to the installed
  equipment.


The installed equipment required for IFR flight (beyond that required for VFR flight)  is listed in 91.205(d) and is mostly equipment used to communicate with ATC and to maintain control of the airplane when flying without visual reference to the ground (so no navigation equipment is specified):


  §91.205   Powered civil aircraft with standard category U.S. airworthiness certificates: Instrument and equipment requirements.
  
  ...
  
  (d) Instrument flight rules. For IFR flight, the following instruments
  and equipment are required:
  
  (1) Instruments and equipment specified in paragraph (b) of this
  section, and, for night flight, instruments and equipment specified in
  paragraph (c) of this section.
  
  (2) Two-way radio communication and navigation equipment suitable for
  the route to be flown.
  
  (3) Gyroscopic rate-of-turn indicator, except on the following
  aircraft:
  
  (i) Airplanes with a third attitude instrument system usable through
  flight attitudes of 360 degrees of pitch and roll and installed in
  accordance with the instrument requirements prescribed in §121.305(j)
  of this chapter; and
  
  (ii) Rotorcraft with a third attitude instrument system usable through
  flight attitudes of ±80 degrees of pitch and ±120 degrees of roll and
  installed in accordance with §29.1303(g) of this chapter.
  
  (4) Slip-skid indicator.
  
  (5) Sensitive altimeter adjustable for barometric pressure.
  
  (6) A clock displaying hours, minutes, and seconds with a sweep-second
  pointer or digital presentation.
  
  (7) Generator or alternator of adequate capacity.
  
  (8) Gyroscopic pitch and bank indicator (artificial horizon).
  
  (9) Gyroscopic direction indicator (directional gyro or equivalent).


As far as converting an airplane from VFR to IFR, the Type Certificate Data Sheet (TCDS) must specify that the airplane is designed for IFR flight, and then you could add the missing equipment to make it qualify.