Well those don't look factory. I have one big filter in the same spot but i don't think it has anything to do with my transmission?
You replaced a pump but was it the scavenge pump or the transmission pump? Fluid in the T/C case should be minimal. The few times i drained mine there was less than a beer can in it of oil.
I'm not sure if they are factory or not but I was at least glad to see there was some kind of fuel filtration. The two smaller ones on the left are the fuel filters and the large one is engine oil. There are actually two different oil filters on this thing as it also has the same sized filter mounted on the side of the engine. I was hoping it might be some sort of supplemental filtration for the TC and was causing my flow problems, but no such luck.
I still have not done much overheat troubleshooting with the machine cutting off too frequently to overheat the TC. I've been working my way from the tank to the PT pump looking for restrictions or possible air leaks. The throttle shaft had a leak as did a loose elbow fitting for one of the fuel lines. I replaced seals and tightened fittings thinking it must be the cause of the problem, but it went right back to its shutoff routine during testing. I learned from cleaning inlets, replacing fuel filters, etc that air being introduced into the lines does not seem to cause an abrupt stop like I am experiencing during operation. Its more of a slow speed decrease as the air is introduced. So next on the list is the electronic fuel shutoff solenoid as it is about the only thing I can think would cause it to shut down just like the key has been turned off. Definitely also seems to be tied to engine temp increase as it rarely happens the first 30 minutes of operation. I'm hoping I have a heat related short in the solenoid circuit.
For the overheat problem, I have been considering buying a hydraulic flow meter to try to pinpoint where I'm losing fluid volume after the fluid heats up. Looks like I can get one for around $200 and it would be a nice tool to have around. I'm going to have to figure out the feasibility of getting it hooked up though. The trans piping isn't terribly forgiving.