Sounds like you might have an issue with the coil packs, check them first, clean all the connections and ensure the earth strap connecting them is clean and tightened up.
Check the spark plug wells, as these sometimes fill with oil from carelessness when topping up, to rocker cover gasket failure.
Might be with having the ecu read, which will might indicate a problem. A garage will do this, or you can buy a KKL cable from eBay and download a copy of multi ecu scan, which should set you back no more than £10 (the basic software is free
Can't help you with the gearbox issues, could be the slave cylinder/release bearing. My old Citroen had a grumble on idle that disappeared when you dipped the clutch, which was diagnosed as worn input shaft splines.
A used gearbox plus fitting, will probably run you in the region of about £4-500 but if it's the clutch mechanism, you might want to add another £250 on top of that for parts.
If you can spare the money, then