Failed to mention whether you have the 1.25 or the 1.42 - AND depending upon your source (if it’s from some “well-known” individual donor here) your machine may have already been well-cleaned and thus, quite possibly…
more than sufficiently
“op-ti-mi-zated”.
Here, all minis are very thoroughly cleaned internally. This especially includes all individual fan blades restored to near-new pristine condition. Additionally, heatsinks are carefully removed, cleaned and then re-pasted. Conventional hard drives are replaced with SSDs (which further reduces internal heat and some need for the higher fan speeds). In addition, small rubber bumper feet are added to the bottom which improves the air temperature intake by raising the mini up from typical flat surface placement, as opposed to that hot, flat rubber bottom of the mini just sitting flat on any surface (and thusly heating the surrounding area from which intake air is drawn).
As the Godfather of Soul sang...
"Get up off-a that thing!".
How’s that for an over-blown and partial "non-answer" to your queries?
As for fan noise between the 1.25 and the 1.42, I really don’t remember much difference after all the above… but I’m not running Virtual PC either. (And if you really want some fan noise in a Mac mini, try one of the early Core2Duo equipped ones. Yowza!) BUT someone, somewhere… recently mentioned the addition of a “copper heatsink” for the mini and a different fan. (Might’ve been dosdude1 and his Mac mini 7448 processor project?)
A copper heatsink for a Mac mini? (Yup.) 'specially for overclock's like @domii 's recent 1.8 GHz Mac mini.
http://macos9lives.com/smforum/index.php/topic,2408.msg46595.html#msg46595AND I’ve not benchmarked performance differences (that I can remember) between similarly-configured, 1.25 & 1.42 minis running v.9 - but I have several to complete re-assembly on here that I should finish soon. And if my feeble mind can remember to do so, I’ll QuickBench two and provide those results.
Meantime, big congrats on your “new” Mac mini!