Sorry, you're out of luck. The only way to get the HK Chassis is to pick up from the remains of one of the HK-50s before T3-M4 leaves the Warehouse. Unfortunately, there is no alternative source for the chassis.
If you want to rebuild HK-47, you will have to reload an older save. The battle is very easy, just equip the Renewable Shield and the Droid Shock Arm, activate the shield as you approach the HK-50s, then attack them with the Shock Arm (they die in two turns each and seldom come close to breaking down your shield).
HK-47 is all right. If you really loved the character in the first game, then it is probably a good idea to repair and use him in KOTOR2. If you were indifferent to his act in KOTOR, then nothing has substantially improved to the degree that is worth another hour or two of gameplay.
However, if you are a darksider and want to maximize your attribute bonuses, adding HK to your party and gaining influence with him can be profitable. You can gain a +1 Wisdom and +1 Constitution bonus (as well as some marginal bonuses to your Saves) by gaining influence with HK-47.