To the OP: The way to put the filter in the tape loop in your pre is to listen/monitor from the "tape in" as the source, while the filter is also receiving the signal from "tape out". If your pre can do this, the tape out would be connected to the input side of the RF-1, and the RF-1 output would be connected to the tape in or tape monitor.
IME, woofer pumping is due to feedback from speakers to turntable - usually because the table is situated where low frequencies collect and reinforce each other, not because it is recorded that way in the source material. But of course, I'm not 100% familiar with your setup.
When you recorded your needledrops, did you monitor the recording through your speakers, or was the amp bypassed? If you we're listening to the LP through your system as you were recording, it may have reproduced the acoustic feedback as well.
Do you notice woofer pumping at low volumes, or only when playing somewhat loudly?
A simple but inconvenient solution would be to put the filter in between pre and amp only when needed. That said, if your needledrops also cause woofer pumping and you are concerned about loss of amp headroom, why not leave it in place at all times?