Anty,
It sounds like you have a torque converter model. Probably rain water in the shuttle compartment.You may have a bad shuttle cover gasket or possibly the adapter plate gasket. Check the shuttle compartment vent integrity, also the dipstick gasket. Melting snow seems to be the worst culprit.
There is an o-ring visible just inside the big female disconnects(couplers), try replacing them.
Probably a good idea to leave the hoe off. Spool seals are known to leak on the hoe valve body. I just replaced the 12 quad rings on mine, it's about a 3 hour job.
I would change your engine oil,and shuttle oil first. Case TCH oil for the shuttle, about 12-15 liters. I would use a good 10-30 diesel oil for the winter, in your engine, or a 15-40 oil year round. I'm just guessing about 8 liters. Check carefully for coolant in the bottom of the engine oil pan when you drain.
I wouldn't change your trans/diff oil for now, just pull the drain plug to check for water. It's at the bottom rear of the transaxle and takes a 1"socket. The dipstick/fill is just behind the trans cover plate. This compartment can have it's oil changed when you pull the differential cover off, for an inspection.
Getting back to the shuttle compartment, there are 2 drain plugs, each with a 1" head, located underneath the machine,one just behind the engine and one just in front of the transmission.The shuttle has it's own dipstick/fill plug, just like the one on the transaxle behind it. Look for it in the right rear corner of the shuttle compartment cover; that's the cover just in front of the trans cover(has gearshift lever).The shuttle filter also has a drain, at the bottom of the housing. This filter housing is located behind the radiator grill. After changing the shuttle oil and filter, run the machine for 5 minutes, then shut-off and recheck the dipstick level.
Other fluid changes could include the power steering and hydraulic systems. Your engine coolant should be checked for strength, if you do not change it.
Yes, your machine uses an oil bath air cleaner. I believe it's filled to the indicated level with motor oil. Check the screen above it for cleanliness, before reinstalling the pan.
Replacing both fuel filters should be included in a tune-up, as well as draining the fuel tank water trap.
I think you will find a used exhaust manifold out there at a tractor wrecker. There are also new aftermarket manifolds available.
Not sure what you mean by rubber bushings. These machines are well known for front wheel spindle bearing failure. Spindles will 'lean-in' at the top, and raise once the thrust bearing fails also. One can sink a lot of money into fixing these up right. Someone here a long time ago used a plastic insert, like PVC pipe to repair a loose spindle.Try curling your bucket down, then raise the front of the machine off the ground a bit. Block the front end up, then remove the front tire, this allow the spindle to drop out, once the steering arm is removed. There is only a toe-in measurement, I will check my manual.Phil