Just made the switch to v2 also and i must say i feel the same, especially the speed of the autofocus has improved it seems, am curious about the dynamic focus upgrade, haven't had the chance to test it yet but i hope it will be good cause i had some troubles using the dynamic focus option on fast moving subjects.
About the focussing issue, let me first state that im also 'catching up' on the digital realm and certainly am not a 'pro' at itm. I do have some experince in the nikon SLR's and some 'low-budget' digital cameras. As a D70 owner i do advise you to look up the 'Thom Hogans Complete guide to the Nikon D70' wich is very in-depth and technical background info on the D70. And contains nice goodies as custom d70 tonal curves to load into youre D70 (not tried it out yet though). At first i also thought my pictures lacked some sharpness but after trying it out on a sunny day i must say i was stunned by the sharpness of it. Though still some scenes en situations i feel a bit the same way as you do. For example Landscape scenes under overcast/cloudy conditions i also feel a little unsure about the sharpness of the pics. But that just as well could be me.
The nikon statement about watching photos in CS is a bit true cause you are looking at a magnified portion of your photo when looking at it at 100%, A pc screen (and especially the lousy one i have hear ;( ) will never be as sharp and clear as when you print the picture out (gonna print my first photos this week so im curious). But the whole focus issue is a little suscepticle(dont know the right word/spelling but otherwise influenced would be the right word i guess) by the whole attention it got with the whole backfocus issue wich must have been revised by now though the hype about the whole focus thing still continues. I've taken a quick glance at the dpreview.com forums on the D70 and noticed a big 'two-camp' stance on the focus thing, some say its there others denie it. I myself am still not sure but am leaning towards the last. Maybe if there are no privacy issues (wich im sure are there in surgical scenes) you can post some pics, if you like (i already have some photos posted in mine and Dennis's thread) i can post some to (Raws pereferably)and you can compare, maybe it is beceause your D70 is older then mine and it hasn't been revised yet.
About the workflow im not sure if upping the sharpening parameter is always better/usefull, it still remains a post-processing feauture wich roughly is the same thing when you do it in Photoshop and will only sharpen edges and not details. Also it can cause some color-shifting to occur (read this in the Thom hogans book) and it will NOT be applied when shooting in NEF/RAW mode. Also a general rule of thumb is that the narrowest apperture will not give you the most sharp images, it is recommended that you take a 1 or 2 stop less narrow aperture for the sharpest images and that is what i usually do. Another thing that may help you get better focus in youre picture is using the 'hyperfocal technique' by keeping in mind the the DOF's range is 1/3 in front of your focus point and 2/3 behind, so focus on a 1/3 distance in your shot, use the AF lock and recompose your scene to get the longest DOF range in your photo.
Hope this helps a bit,
Jape,