through the shifter is the easiest!
there is a filler plug, but youll need a little hand pump to use it (from what i understand)
check the manual as to how much gearbox oil you need, i think its 1.9L, but check to be sure.
engine oil you fill it up till the dipstick sais its full.....then run engine and check it again.
assuming your talking about 4age, i use penrite hpr15. semi synthetic 15W-60. works good and not to thin. ive never used engine flush, they reckon diesel is good.
i woudlnt worry about changing your coolant if you are not having overheating issues, its not really a maintenance thing, if its still green its still good. don't fix something that isn't broken!
if its a 4ac change points if they are burnt out and possibly spark plugs if they arent looking so good. at least reset the gaps on both.
an 86 isnt any different to any car......change oil and oil filter and it will be happy.