I realise I only mod BC but the concepts is the same so here's my 2 cents:
I would scale all cannon vessels to their canon lengths based on these charts:
http://www.ex-astris-scientia.org/fleet-charts.htmFor kitbashes, measure the saucers off the cannon ships to get their length, since we know it would be much more dificult to make saucers of different sizes that look identicle than a nacelles or torpedo pod. For example, I scaled p81's ambassador to it's caonon size. Measured the saucer of XXXmeters. Then whenever I do an ambassador kitbash, like mackies warspite, or knox's uss aleric, Belmont, or other such ship I make the saucer the same length, and they look nice that way.
As far as non-canon ships, especially romulans and klingons, Decide what role you want the ship to have, and find a canon ship of simila role and make it close to that size. (in otherwords, just guess) Everyone has a different opinion when it comes to non-canon ship size, and if they're going to b***** they're going to do it no matter what size you pick.