Try junk yards for the cowl. Depending on the yard you can sometimes get them dirt cheap, other times they'll cost about $50 (still half the price of a new one).
The water pump is still a possibility, so's a leaking rad cap (do the test I mentioned for this one and a free way of testing for air coming into the cooling system some other way... do a pressure test on the cap to be certain of the cap, most auto parts stores should have the tester you can use for free).
Ask your mechanic if they ever checked thew timing and if so ask what it was set for. It should be set for 10?BTDC.
The sluggishness and bump could be a few different things and I've covered those in your other thread(s).
Air can remain trapped in the heater core. If the core is being bypassed (in the case that I already mentioned) then it may take ages to get it all out. Get the heater core flowing again and the system should burp any remaining air in just one or two drives.
The brown murky color was probably actually rust.. it is a cast iron block... old, incompatible or improperly mixed coolant can cause this. I highly recommend you thoroughly fluch the system and use Toyota's red coolant.
Do this tonight: Take the oil cap off and look in the underside of it... is there any brownish sludge resembling chocolate pudding? If so, you're most likely looking at a BHG.
pH test strips like those sold
here can be used to pretty accurately determine if your HG is venting compression gasses into the coolant system. See if you can find some locally.