A lot of those questions are answered in this thread:
Let's hear it for the Leitch DPS-290But:
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1. Fan noise wow, is it ok to just disconnect fan? I would rather replace with something MUCH quieter, does anyone know what size it takes?
You can disconnect it if you have good airflow around it, otherwise get a new quieter fan. Diameter is written on the fan.
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2. Comb filter, how good is it? I have only played around for a bit but I don't seem to notice a difference between using the DPS-290 comb filter vs using the comb filter on my DMR-ES15 DVD Recorder?
The DPS-290 has a very good 2D comb filter. It's good but won't beat out a properly implemented 3D comb filter. FWIW 3D filters spend a lot of time in 2D mode in video anyway.
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3. Can anyone explain some of the settings? Some things are obvious but I have no idea what to do with Y/C horizontal control, vertical blanking, burst status, doc status, advanced sync, Y/C vertical delay or VITS Comb Control. I have read the manual and know how to change these but no idea what they should be set to?
Just leave all that at default. You may have to adjust Y/C delay if your player has a slight mismatch between luma and chroma.
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4. Where in the chain do most people use these? Right now I have DVL-90 composite --> DPS-290 Svideo --> Key Digital Scaler HDMI --> TV but I also tried DVL-90 composite --> DPS-290 composite --> DMR-ES15 Svideo -->Key Digial Scaler without seeing much of a difference, am I putting it in the right spot?
If you're using a scaler, it should go right before the scaler. S-Video out of the DPS-290 into scaler