When I upgraded a 26g to a 40B, it was going in the same spot, so I had to tear down one, move it out, set up the new one with a new stand. Here's what I did that would also work for you just changing substrate, although you're not moving one tank to make room for another. Should only take a couple of hours and your fish will be fine in a temp tank for that long provided you move the filter and heater with them to the temp tank.
I had bought 20g tank for $20 at Petco sale. Moved my kitchen table near to where the 26g tank was and put the 20 on that. Siphoned about half the old tank water from the 26into the 20 and filled the rest with new conditioned water. Moved the fish, filter and heater to the temp tank - no deco.
Finished emptying the old tank of water, the plants and most of the gravel, moved it out of the way, set up the new 40B, and went to work on this one, adding all new substrate, driftwood and plants (I used mostly silk for this tank). Added new heater and new filter. Filled with all new water using Prime, close to the temp I wanted. Got the filter and heater going, moved the old filter from the temp tank back onto the new tank and moved the fish into this new tank. By keeping the original filter on the new tank along with the new filter, there was no cycle and no problems with the fish. All are loving their larger home.
I wouldn't worry about getting the temp tank fixed up until the 29 is redone and fish are back in there. Just move your fish, filter and heater to the bare temp tank while you work on the 29g. Then you can work on the 2nd tank at your leisure.