I would suggest that you store and retrieve, rather than trying to down-link your data in real time. It gets cold in the upper atmosphere, so you will need to insulate and heat your electronics. GPS will get funky above 40000 feet, radio communications will be sketchy at all altitudes. Monitor the high altitude wind speed and direction so you know where it will be. If you use a weather balloon, you will be able to see it up to 100,000 feet if you know where to look.
Temperature and pressure are easy. Get a couple sensors, and save the output to the eeprom, or an sd card.
Position - GPS will work once it has returned to ground. Use a beacon that turns on once it’s down and sends you the location. Trying to keep up with airborne telemetry will be a headache, especially on your first flight! (They have high altitude GPS devices, but they are expensive and not as easy to use as the GTop and UBlox devices that are commonly used in amateur devices. If it gets into your blood, think about investing in one of these, so you can track it in real time.)
Altitude - get an altimeter breakout. It will take T and P into consideration. Record this as well, and read it after landing.
First thing to get is a balloon. A latex weather balloon will get to 100,000+ feet when filled properly. Other balloon stuff is the filling rig - you can use helium or hydrogen. Hydrogen has the advantage of about 20% more lift, and 1/100th the cost. It’s disadvantage is that it is flammable. Once your balloon is aloft, this isn’t a problem. On the ground it requires strict adherence to safety procedures. Every launch I have been part of has used H2.
The next thing is a site. Your balloon can travel some distance. Launch on a calm day to limit it’s range to 10 miles or so. You want to avoid populated areas, air traffic lanes, and restricted airspace. Get FAA approval for your flight if you are in the US.
Design a harness - the balloon goes up, and your device will dangle from a sturdy line. The parachute mechanism also hangs on this line. As the balloon ascends, the pressure and the temperature both go down. Reducing the pressure causes the balloon to expand. Cooling coses contraction. The altitude vs diameter function is complex. Use the real gas law for the lift gas in your calculations. Your balloon will have an approximate maximum diameter. Once that is exceeded, the balloon pops, and the payload drops. If you put baby powder in the balloon before filling, it will leave a white puff in the sky when it pops. It’s about 20 miles up, so look carefully.
Make your capsule - at moderate altitude (40-75,000 feet) it’s 40 below, so everything is going to freeze. Your box needs to insulate your electronics, as well as protect it from a high speed landing and dragging. Put some sort of heater inside. Styrofoam is really good material. Fiberglass with insulation glued on the inside is the best for strength, durability, and (depending on the material and thickness) the best insulator. It is also orders of magnitude more expensive. If you want to reuse your capsule, make it sturdy!
Keep your circuitry and mechanisms simple. When it’s cold it will be brittle, so limit movement, and it will contract and expand considerably. So it should be a bit flexible as well. Power will be an issue because of the pressure and temperature changes. Try to keep the internal temperature (slightly) above freezing, and use solid construction batteries. Remember, if your power fails, so does everything else.