I try to do this all on the same day if possible. Continue to keep an eye on environmental data, especially temperature. WIND INPUTS MATTER in 4DoF. You need to have roughly the correct windspeed and direction because they will cause both windage and elevation changes. If you ignore the wind those small elevation changes will eventually add up and frustrate your day.
I zero at 100yd (or 300yd using zero angle-- see blue paragraph below) with 20 rounds. This is mostly to get solid MV data off of a Garmin or LabRadar (ideally). Magnetospeeds are typically pretty close but can vary within 15-20 fps in the worst cases we've seen. Garmins and LabRadars are usually +/- <1fps on the average as compared with our big doppler head. A 20-round zero also ensures my zero is where I think it is, and you'll notice dramatically less "zero wander" when you do this. 5-shot and even 10-shot zeros can walk around a bit. Plug enough rounds into the group and you will see the true MPOI... Is the dead horse beaten yet?
At this point I'll fill in all of the info for setting up the profile, Twist rate, MV, scope over bore (Measure this at the objective lens-- that's where the image you look at through the scope is generated), and the bullet you're using. You can do Zero angle at this point but I usually just leave it at 100yd zero range.
With the file built and a notepad and pen, I record the environmental and wind data and shoot AT LEAST 10 rounds at a clean piece of steel or paper target at 300-400yd, then again at 500-700yd, then again 800-1000yd. At each distance record what was necessary to get the MPOI to line up on the waterline. For example if it says to dial 8.2 mils but I'm 0.15 mils low, I record 8.35. Also record the windage necessary as it can be useful to back-calculate the average wind speed for the duration that I'm shooting.
So now with a solid 100yd zero and MV and 2-3 other yardlines of solid data I will go into the program and address inconsistencies if they exist. Usually using this method results are pretty spot-on to 600yd then you start seeing some vertical creep and that's where I'll adjust with axial form factor. If I used a magnetospeed or optical chronograph, or honestly if I don't even have a chronograph, I will adjust MV off of the <600yd data, then form factor off of the >600yd data. I have had pretty good luck using 600yd 4DoF dope as a chonograph and getting within ~10-15fps of the true average. YMMV.
Also, I've been making it a habit lately to set my zero angle off of a 300yd target. I think this gives better resolution and less chance of things like parallax error and lighting conditions screwing with the results. I like my turrets zeroed somewhere near the 100yd zero so that I always dial up, but you can get a rough 100yd zero then jump straight to 300yd to get MV data collection and set a zero angle instead of doing it at 100yd. Just tell the program you hit X.Xmils low (usually 0.9-1.2 range, will depend on your setup) at 300yd when you set the zero angle. Hopefully that's clear as mud.
The important thing is to keep tabs on accurate data collection of as many of the variables as you can and WRITE IT DOWN. Nothing like spending an afternoon getting frustrated chasing your tail around with this stuff when you forget what you've done.
When I'm all done there, I usually run back to a close, medium, and far target and verify.
Form factor is, for the most part, a set-it-and-forget-it feature. It may degrade slowly over the life of the barrel. If you question if your axial form factor has changed, verify zero, verify MV, and shoot at a 1000-1200yd target for 10-15 shots and note vertical MPOI.
