I will address this in two portions:
TECHNICAL VIEW:
I think the most important thing to increase would be the bitrate rather than the sample rate. If you are recording in 16 bit, I usually recommend increasing the bitdepth to 24 bits in order to lower the noise floor (120 dbs), thus giving you more headroom.
If you have high end converters that correctly make a signal represent 44.1/16, then there shouldn't be a problem recording in 44.1. However, I think that cheaper 44.1 converters are not as good as cheaper 96 kHz converters, because in 96kHz converters, filter response artifacts are bumped higher up in the audio spectrum, thereby skirting the actual issue, which is poor converter construction. So, cheaper 96kHz converters are generally "better" persay. However, I would choose hi-quality 44.1/16 converters to the 96's. (Actually, I would choose hi-quality 96's but lets not get into that!
)
But, the fact is that 44.1/16 is CD quality, and its great, if you know how to properly engineer the recording. A slightly higher sample rate of 48kHz gives you a little more to work with than 44.1 and allows for more ultrasonic frequency (vis-a-vis the human ear), so some people say you gain a little bit more alleged ultrasonic "textures", but not increasing your file size to massive extremes (as 96kHz and 192 kHz recordings do.) In reality, 48Khz may just sit better with the soundcard you are using and have little sonic fidelity recognition anyway.
The human ear can't hear over 20 kHz. So anybody talking about recording 96kHz/192kHz SPECIFICALLY for CD at 44.1/16bit is being paid by someone.
PRACTICALLY:
In your case, increase the bit depth. For the sample rate, 44.1 or 48 should work for you, depending on what kind of soundcard you have, and your system resources. Remember, that at any higher sample rate than 44.1 you have to have a good sample rate converter that has good anti-aliasing filters to downsample to 44.1.
The fact of the matter is that, most people can't make good use of 44.1/16 anyway, because they can't engineer.
There is no advantage to SRC from 44.1 to 96, which is what you were doing. It also shows that you may not really grasp the concept of samplerates and bit depths, perhaps. Read more on the mathematics involving sample rates, like the links posted above. Also, most people don't have the audio chain to support the "quality" of higher sampling rates, which is claimed by many audio pundits. Think of all the car factory audio systems and how awful some music sounds, because the speakers can't represent the frequency ranges in what is generally a good recording. PEOPLE CAN NOT TELL THE DIFFERENCE BETWEEN 44.1kHz recordings and those at significantly higher rates. Also, if you are recording poorly, through a bad microphone, then the point is moot as well.
ALSO, I usually record at 96kHz/24 bit but that's because many projects are now being put not only on CD, but DVD as well, so I have to have the quality of file to support what is demanded. Also, with people trying to force SACD down your throat, the file quality has to be "better."
Work on your engineering, though. Read and learn more!
Sincerely,
God