I have done what you are looking to do with your windows, but with one big difference. It was an exterior door that was 1 3/4" thick. A considerable bit more room to add insulated glass to. Your glass cost will be considerable, and as others mention, they will need to be assembled by a glass company.
To recut the seat for the glass, I used my router set to the new depth and a flush bearing guide, so I could use the original edge that the windows set inside to act as the guide for the flush cutting router bit. After that I still had to cut out the radiused corners left by the router bit with a chisel so the glass would seat in all the way. After all that trouble there was just a marginal amount of room to set the beading after the glass was in place with the sealant. Quite the pain, IMO but it got done. There were only 9 pieces of glass to redo, it was a 9 lite door, glass only on the upper half.
If it were me, even if I had all the time in the world, for what you are looking to do, I would get window kits that replace the counterbalances of what ever the nature you have, whether it be springs, strings or sash cord with weights inside the jamb.
Several window producers make these kits to for standard sized windows and they slip right in... kinda. Remove the interior window stop and old jamb liners if you have them and the sash along with them or if you have sash weights they can be removed after the window sash are removed, there is an access to get them out. Insulate the cavity after you get the weights out.
To install can go a few different ways depending where you get them from, The ones I seen from Marvin, a few clips are installed to hold the jamb liners in, the liners are set in place and the sash tilted into the opening. My description is an over simplification, but I hope it gets the idea across.
One last note, I would do this only if you window jambs are in tip-top shape. Sills are typically the weak spot here.
