I have seen them with the filter and without it. Both function the same in any case. The filter is not fine enough to catch much except for a large chunk of something; in that case, you probably have bigger problems than just injectors clogging.

There are people on this site that do injector work. Maybe you could contact one of them and see if the injectors are salvageable. If the shop was so unclean, they could have contaminated and scored the nozzles as well. It sounds like the disassembled the injectors and did not lap them each time upon reassembly.

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1991 F250 super-cab 7.3 IDI. (rebuilt by me) Banks Sidewinder turbo, hydroboost brakes, new IP and injectors.
2003 S430 - 107K
1983 300SD - Tanoshii - mostly restored ~400K+.
1983 300SD - Good interior. Engine finally tamed ~250K.
Monark Nozzle Install Video - http://tinyurl.com/ptd2tge