The crank seal is right behind the crank timing sprocket (the cogged one that the timing belt goes on). The oil pump drive shaft seal is behind the oil pump drive gear. If the cover you are talking about is the aluminum lower timing cover then yea it has to come off. If you are talking about the inner timing case, no that does not have to come off (its a BITCH to take off anyways) but it makes replacing the seals alot easier.
The front crank seal is not that hard to replace, as long as you use the SST. If you don't have the SST then be careful not to scratch the crank or all this work will be done in vain. But the oil pump drive shaft seal is different. The TSRM says to cut off the lip of the oil seal with a knife and then tape a screwdriver and pry it out. There is no SST to remove the oil pump drive shaft seal. I've never replaced an oil pump drive shaft seal on these engines so good luck.
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