Should I have the raw buffer on or off? Also under the quality settings in chdk what should I set that to?
None of these will affect noise. Raw buffer cached will speed up DNG processing, otherwise makes no difference. The CHDK quality override only enables you to choose "super fine" quality on cameras that don't support it, and this generally just results in a larger image without visible improvement in quality.
Another problem I am having is that I will set the iso to something and once I review the picture and check what the iso was set at for the picture it will be some oddball number other than what I had the ISO set at. For example last night I just took a picture in my room with the lights on and had the iso set to 15 and exposure set to 2 seconds. The picture came out really clear with very little noise but when reviewed the ISO shows it was set at 26!?!?
For unknown reasons, Canon uses two different kinds of ISO numbers, "real" and "market". The "market" values are used for display, but for technical reasons, CHDK uses the "real" values for ISO override.
That said, I'm not aware of any CHDK cameras that are actually able to override ISO lower than the normal Canon low value. The only way to verify this is by comparing image data of otherwise identical exposures (ideally raw, but jpeg is probably valid in most cases). The override value appearing in camera displays or exif should not be taken as evidence the override worked.
If your subject allows, stacking multiple exposures is a good way to increase SNR. Aside from that, there's really not a lot you can do given a particular exposure length and ISO, this is the price you pay for lots of megapixels on a tiny sensor and no software hack is going to fix it.