Hi I do not think you can use both. It will be either short circuit protection and the power supply will stop. You have to switch off and wait for the bulk capacitor to discharge then switch on again for reset. It will be better if you use a current transformer for short circuit protection. If you used my pcb then you have space for it. See attached fig below
EE42 transformer I dont think is large enough for 1000w. There are two types of EE42 one is 42/21/15 and the other 42/21/20. The first one has a maximum power of just over 1000w at 65kHz and the thicker one is just 1300w. You are a little bit limited here as the cores are very close to the wanted power and they may saturate. I suggest you will use ETD49 core which is more suitable for this power
The first prototype of my smps uses a current limiter. This also create a soft start for the secondary capacitors to charge up. Unfortunately it does not work for short circuit. The IR2153 does not have soft start and there need to be another way to charge up the secondary capacitors and even to cater for when starting the smps on load
The IR2153 may not have enough drive current to switch IRFP460 (only 180mA) and at least you will need some kind of arrangement to boost up the drive and discharge current. You will need at least 1 to 1.5 amps to drive IRFP460 properly. Do not be fooled if it works on light load as when it comes to heavy current the fets will need a good drive and if they dont find it they may heat up and explode.
You will also need a better auxiliary current and also a better start up circuit. The way this circuit is configured is not suitable for more power. I guess you will be better off making Ludo's version for 1000w