Exhaust repair is really hard to estimate, and that's why RepairPal does not have exhaust jobs listed in many cases. If you want to make a comparison, I would get the parts costs they are quoting you, and compare with prices you can find online. I've heard technicians recommend replacing these exhaust components instead of trying to weld and repair them, as some shops will do for customers who want to save money.
Yes, it is advisable to replace the water pump when doing a timing belt, just because the pump is not that expensive, but the additional labor is very small. If you do a timing belt, and then a month later need a water pump, you are out the same huge labor bill twice.