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Alright
1. "Is this supposed to be sealed?"
That is an inspection plate. It just covers a tiny hole that allows you to see into the bellhousing.
2. When you turn an SR20 upside down the lifters all bleed out. So now you will have to remove the cams and lifters, and bleed the air out of them, before you re-start that engine. Never turn the motor upside down (or let the lifters sit sideways) for this reason.
3. Measuring a rod bearing is not going to tell you much, unless the whole engine needs to replaced. chances are that if the bottom end is in "trouble" then it is one bearing, often a single random rod bearing, that is in trouble. And trouble is visual, the bearing would look scored or ruined. "Plastigauge" is not a really useful tool for someone in your position. I am still in agreement that you could pull at least one bearing (either rod #1 or #4 IMO) Just to see that is looks decent. But I would put it right back to the torque you found it (FSM) without the use of plastigauge.
finally, all the gaskets you see are just silicone. I would use Toyota grey (or permatex grey) on all the oil pan / water pump gaskets. One big noob mistake is using too much; I recommend you practice on another object to see how little it really takes to seal something up. Excess gets squeezed out, and can wind up in your oil strainer (pickup). Another noob mistake is going too tight; make sure you follow FSM torque, it does not take much tightness to get a good seal and overtightning will cause leaks and in the case of your thin pan, bent mating surfaces.
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