I am running a Stratasys Dimension 768 SST, with a "rebuilt" extruder (dual setup includes support + model). This extruder, basically, follows the OEM design with exception to the tubing diameter (few mils smaller for rebuilt, although there is a generous inlet taper and/or bushing, larger than the filament diameter feed stock) and the way the tubing has thermal contact with extruder body and cartridge heaters. The OEM design, apparently, had some thermal epoxy to "bed" the 2 nozzle tubes, which are brazed into the nozzle tip block. The approach, I am using, is Al foil packing around the SS tubes, tight to the Al extruder body (still brazed connection to the nozzle tip block). I had no choice but to recondition the extruder, because of a breached nozzle tube. In any case, with a cleared out nozzle inlet to start each time, I do get transient extrusion at standard temperatures of 250 (support) and 280 (model ABS), and in an adjusted temperature range, with some preliminary experiments. I clear out the nozzle inlet with a metal pin, down to the tube bend (I don't get why the design had this problematic 90 deg bend radius close to the cold end, feed wheel!) For the support, the extrusion goes for about 5 secs, then slows down, and the support filament feed stock stalls and strips out the filament, turning it into white debris. For the model, the extrusion goes longer for about 20 secs, and also slows down, and, in this case, the model feed stock splits and gets fed outside the nozzle tube inlet, but no white debris in this case. This cycle may be repeated by cleaning out the inlet clogging with the stiff metal pin.
I realize this is not a perfect description of the system, but I am hoping that someone who knows this extruder configuration or a similar one (system is quite old, unfortunately), may chime in here with suggestions. I will add, that I am running the system in a so-called maintenance mode and have some minimal adjustment of the firmware (like the hot end temperatures - defaults mentioned before) for the build mode (which is only during actual part run).
Thanks in advance for your help or suggestions!
Here are some diagrams/link to descriptions for the extruder as well:
My exact extruder (i.e., head) system: http://www.amtekcompany.com/pdf/dimension_bst_sst_elite_768_head_clog_guide.pdf
A similar extruder (showing heaters, extruder body to isolate model & support paths, tips, and thermocouples) https://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwifyLnJsu7OAhVIOCYKHaSIDLQQjRwIBw&url=http%3A%2F%2Fwww.3dprintforums.com%2Fshowthread.php%3Ft%3D2237&psig=AFQjCNGM1BTAiWzUn4fNJ8-z5HDWxa6OEQ&ust=1472824417165187
This site shows another user take apart/redesign the extruder in question (pay attention to the 90 deg bend in the nozzle tubes) (see attached picture)
I also have a few documents: user manual, service manual, etc. that I may share, if I knew how to upload to this website.
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).