I'm an MTB rider who occasionally got into a Road Bike for 60 km rides. (5 hours aprox). From experience I would advise several short rides before a very long one. Ride until you feel uncomfortable and keep going for another 10-15 minutes but don't let yourself get into [severe] pain.
For example: Get two 30+ minutes a week for 2 weeks, then grow to two 45+ minute rides a week for another two weeks. So in a month (+/-) you'd be ready for a 1.5 hour weekend ride. After that you grow as you see fit. (These numbers are just a rough reference).
Also, if you are a casual (read non competitive) rider, do not set the bike for the most aggressive position, that is, set the stem angled upwards and choose a short one, place the stem spacers bellow the stem to raise the handlebar.
As you get more used to the bike, you may want to progressively make changes (adjustments or component swaps) towards a more aerodynamic position, but for starters, I recommend setting the handlebar such that the flat part of the handlebar is at the same distance and relative height from the saddle as your MTB (or as close as possible).
Indeed MTB and Road bike geometries are very different, but the measurements I found to be more relevant (regarding pain from not being used to them) are the effective distance from the saddle to the grip point, and the height difference among them.
That means that measuring top tube, stem, etc. is a bit fuzzy and of less practical value for the casual rider. Instead, Measure the distance from the center of the saddle (roughly where your sit bones rest while riding) to the point where you actually grip the handlebar.
For MTB you got only one grip position, but for road you have at least four: On the flats, on the drops, on the hoods and on the "corners" of the handlebar. Most frequently the rider that comes from an MTB geometry would spend more time on the flats and will progress towards the hoods.
With that in mind, if the road bike has the chosen grip position further away from the saddle and/or lower (compared to the MTB previusly ridden) then the torso will be at a lower angle, puting more weight on the arms and needing more effort to keep the head up.
Regarding this last point: Use a road specific helmet or remove the visor from the MTB one. This is because the visor usually found on MTB helmets is designed to be used with an upright head. On a road bike you would have your head leaned forward, so helmet's visor, if any, gets in the way, forcing you to raise up your head, putting additional strain on the muscles of the back of the neck.