A different, but somewhat related question Unravelling Cassini's “ball of yarn” orbit around Saturn, tabulation of propulsive maneuvers? has an answer you may find helpful.
This answer to the question "How to calculate the planets and moons beyond Newtons's gravitational force?" might be helpful as well, though it sounds like you've got the integration under control.
Also be warned that the reconstructed parts of historical trajectories in Horizons can have numerical artifacts that look like propulsive maneuvers but aren't. See Is this what station keeping maneuvers look like, or just glitches in data? (SOHO/Horizons)
Also see Why do the LRO's orbital elements appear to constantly oscillate - except recently?
Looking into the data available in JPL's Horizons for Voyager 1 and 2, you will see that these may not precicely represent what you might first think that they do. Patched conics are an approximation and there may be very large glitches when "spheres of influence" boundaries are crossed that are not real, or they may have been numerically smoothed-over afterward, making them "patched and smoothed conics" ;-) See also How to best patch my conics? and the several helpful answers there.

Revised: Jan 21, 2015 Voyager 1 Spacecraft (interplanetary) / (Sun) -31
http://www.jpl.nasa.gov/missions/voyager-1/
BACKGROUND
See the web-page above for extensive information on the Voyager Mission.
SPACECRAFT TRAJECTORY:
This trajectory is composed of two merged sections:
#1) 1977-Sep-5 to 1986-Jan-1:
A patched conic mission-design type trajectory in which the conics
were constructed to approximately match specific events (such
satellite encounters), providing a rough accuracy.
#2) 1986-Jan-1 to 2031-Jan-1 (pfile_a54206u)
Time-extended trajectory provided by Voyager Navigation
Revised: Jan 21, 2015 Voyager 2 Spacecraft (interplanetary) / (Sun) -32
http://www.jpl.nasa.gov/missions/voyager-2/
BACKGROUND
See the web-page above for extensive information on the Voyager Mission.
SPACECRAFT TRAJECTORY:
This trajectory is composed of two merged sections:
#1) 1977-Aug-20 to 1989-Oct-01:
A patched conic mission-design type trajectory in which the conics
were constructed to approximately match specific events (such
satellite encounters), providing a rough accuracy.
#2) 1989-Oct-01 to 2031-Jan-01 (pfile_m05016u_V0.2):
Time extended trajectory from Voyager Navigation