First, there is a coolant passage in the throttle body. It's there to aid in engine warm up. There is no coolant passage in the intakes, upper or lower.
Remove the throttle body and check it very carefully for cracks. You'll be able to see the coolant passage very clearly by following the tubing inserted into the body.
Second, the bolts are as follows:
Torque is 15-lb·ft for all bolts going into an aluminum thread on the head or intakes, nuts are the same.
The old Toyota part numbering system has the bolt grade, thread size and length in it. These bolts are both a grade 6, M8x1.25 (the pitch is a JIS standard and is not in the part number). The new Toyota part number system uses an anonymous part number; you have to know what it is to know what it is.
The longer is an M8 x 28 long JIS hex head bolt
The shorter is an M8 x 25 long
These bolts are readily available in the dealer warehouses across the US. Talk to your dealer parts specialists about your needs, and make sure you use your VIN and describe exactly what you need. If you only give them a part number, it's up to you to know whether that part number is good or not; they won't bother to try to find where it's used or what has superseded it, unless they're very good, and there are very few of them around.