Silly question WRT the Helios; What sort of adapter are you using?
Most SLR lenses are 'retro-focus'; the mirror housing begs placing the lens further away from the focal plain than the actual focal length of the lens; using dedicated lenses designed for the mount, they retro-focus to account for that extra length in the mirror box.
M42 to Nikon F, though the lens is pushed further away fro the focal plane, and more by the actual adapter, acting like an extension tube; ie it can bring the ear focus closer, but you loose the ability to focus on infinity whilst calibration of the focus scale gets screwed.
Hence there are two types of M42 adaptor for M42-Nikon F; a simple adapter that has F-Mount bayonet to fit to camera, and M42 screw thread the other to take the lens. These will give you focus issues.
Other type are 'infinity corrected' and have a correction element in them; they are a lens as well as mount adapter; still have F-Bayonet on the camera side, and M42 thread lens side, but bit of glass in the middle, corrects the infinity focus adjustment, so the near focus gets pushed back in cal, and you re-gain the infinity focus of the lens.
This may account for 'some' issues.
All example shots, other than the Bubbug, are quite close focus and I presume wide aperture shots; DoF WILL be getting very very thin with them; and if you are close focusing off-scale from lack of infinity correction, even more so, and they aren't 'really' such a great example of the 'problem'.
As to the shutter speed suggestion? old rule of thumb was 1/focal length for hand holding. On a zoom, that tends to be longer and less steady with extra length in the lens, regardless of the focal length set, suggestion was to err towards 1/max focal length, even if shooting at the wide end of it.
But it IS merely a rule of thumb. I have done a shutter-speed limbo with the 18-55 with my daughter, when she was starting her O-Level course; I could hand hold at a subject distance of about four-feet, down to around 1/8s and VR made no discernible difference. Daughter was learning and getting down to around 1/30th maybe 1/15th; O/H 'shaky hands' struggled to get beneath 1/50th! And VF really DID help her get even that low! So the 'rule' isn't hard; camera holding technique, and knowing how steady your hand is; knowing your lens and how low you can go is what matters.
As to the cop factor? Err... yeah... if you start with the rule-of-thumb as guide, then erring on the side of effective focal length to push the shutter speed up does make some sens; especially working with manual focus non VF lenses; B-U-T the lens is still the same physical size, the 'balance' of the camera isn't effected by the crop factor, and unless you are using very long lenses, like my '300mm true-focal length prime; you aren't pushing the balance that much further forwards, and the framing shouldn't be getting 'that' much tighter.... within the limits of how well the rule of thumb 'holds' anyway; the effect of the crop factor probably does't meed to be given much consideration knowing your shutter-speed limbo limits with any lens, make mockery of it anyway, and by the time you are pushing the margins with very long high effective mag lenses, the rule was probably starting to fall down anyway. Probably more signifcant if using legacy lenses on MFT with even greater CF and a lighter camera in the 'dumbbell', more so still, on a micro-sensor bridge with enormous effective reach from bult in super-zoom lens, at greater zoom's.. but... matter of understanding the 'principle' not following the rule to the letter!
BUT, last message somewhat lost; you are still trying to focus with the view-finder & screen! BREAK the dependency! 'Just for Fun' grab a tape measure; grab a chair or something, stick camera on the tripod the back garden; use chair as subject... sit on it if you have a remote! Using the Helios; try focusing 'blind' by guessing the focus distance and shooting to scale NO PEEKING! Do that for a few different subject ranges; then try again, doing it with a tape measure... see how accurate your focus scale may be, with or without infinity corrected adapter.
Then go back to your holly shot; camera on tripod again; and using the DoF brackets, pull focus close, and push it far with a wide aperture; then JUST to humor me... try setting a more moderate aperture, say f8.and pull the focus forward almost as far as it'll come, about 55mm looking at my Helios!.. then work it back until you get the Dof dropping off behind your holly where it is in your example shot, but observe the near leaves stay in the DoF zone.. again, do it BLIND to the scale, DONT PEEK... get a series showing the DoF zone shift; master the machine, don't let it master you! Learn how little you need 'rely' on the aids they cram into them all, and how you can exploit NOT doing what the camera tells you!
Just for fun:-
I took that completely 'blind' with my little XA2 film camera; Black thing i the corner is the saddle bag on my motorbike, I was riding! Shot with the camera in my left hand, under my arm-pit; whilst watching the road as I rode, NOT looking through the camera at all!
YOU DON'T have to look through the peep-hole or obsess at whats on the screen! Worry about what's going on in the real world!!!
Whole set, there were shot with Pops old Zone Focus Retinette, with NO focus aids, not even an accessory range finder; focus entirely by guesstimate of range set on the focus scale, with a little judgement how much DoF I needed around it!
You DON'T need to get paranoid about what you 'see' through the view-finder! Worry about what is going on in the real world!