Loss of extrusion in Stratasys FDM liquefier
This isn't a "turn this knob and all will be well" answer, because your machine setup sounds pretty unique to what most people will have experience with. Not being familiar with the older Stratasys printheads, but based on my overall experience with 3D printers, there are three things that could be an issue:


The nozzles are obstructed. The way you talk about clearing the jams of pushing a tool up through the nozzle end would not effectively clear a jam, it would only push the debris back into the print head, just waiting to be pushed by the plastic back into the nozzle. It could even be a piece of aluminum foil from the rebuild process. The typical way jams like this are cleared is to do a "cold pull" where you heat up the hot end just enough to be able to pull the plastic out, before it has really had a chance to liquify, hopefully trapping the debris in the plastic, then cut the end of the plastic off and reload. The 90 degree bend in their design may make this very hard if not impossible to do.
Heat creep. The tubes are a slightly smaller diameter, and if heat is creeping up the print head and letting the filament expand in these tubes, it may be expanding enough that it will no longer move through the print head. Diagnose this by letting the printer jam, then cool off for a few hours. If you can print again for a short time period before it jams again, this may be your issue, where as an obstructed nozzle would not allow any more filament out. Either turn down your temps, or increase your cooling on the print head to address (or get the original size tubes if possible).
Print head temperatures too low for the print speed. The Stratasys Fortus 250mc I use runs ABS at about 300 degrees. Many of the reprap printers run even higher than this for ABS. The other thing to remember when ever you see people mention what temperatures they use, is that this is relative, and only a guide, as what the temperature reads at the thermocouple or thermistor is usually slightly off from the temperature that is melting the plastic based on heater location in relation to the plastic and thermistor. This can be diagnosed by printing until it jams, pause the print for something like 30 seconds to let the hot end melt more plastic, and then resume printing. If resumes proper printing this may be your issue (and it will jam again shortly if you do not adjust temps).