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Are these correct? What do they mean? I think only #1 and #2 makes sense because for #3 and #4, if you assemble the motorcycle, obviously you're not going to have a new bike ready to go.

1. By the time you assemble the motorcycle together you would have had a new motorcycle all ready to go.

2. By the time you assemble the motorcycle together you would have a new motorcycle all ready to go. (What does this one mean compared to #1?)

3. By the time you assemble the motorcycle together you will have had a new motorcycle all ready to go.

4. By the time you assemble the motorcycle together you will have a new motorcycle all ready to go.

Thanks.
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This is a bit confuing at the moment as none of them really make sense with the start 'By the time you...'. Can you check the excercise please and see if the orginal uses this phrase, or whether the later 'would's and 'will's are actually 'could' as then it all makes sense..
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Correct way to say #5:
There is no point in organizing them.

#6 is not correct. You must say 'them' because you are referring to 'boxes.'

I would just say something like this to the manager:
There is no point in organizing them on the ground because that will take just as much work as putting them up on the shelf.
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Comments  
"by the time" plus a present tense (like "assemble") requires "will".
Generally, only "will" accompanies the main verb if the verb is a static verb (like "have"), and "will have" accompanies the past particple of the main verb if the verb is dynamic.

By the time you assemble the motorcycle you will have a new motorcycle all ready to go.
By the time you assemble the motorcycle you will have learned a great deal about the inner workings of motorcycles.

The backshifted versions are easy to construct. "by the time" is accompanied by a past tense, and "will" becomes "would".

By the time he assembled the motorcycle he would have a new motorcycle all ready to go.
By the time he assembled the motorcycle he would have learned a great deal about the inner workings of motorcycles.

Of the four shown, only the first is used much in real, everyday conversation.

CJ
Scenario: I'm putting some boxes on the ground and I'm going to put them up on the shelf afterwards. My manager comes in and tells me to organize it first so it won't look so messy and I say:

1. There is no point of organizing them because by the time I have done organizing the boxes, they will have been up on the self anyway. (What does this one mean?)

2. There is no point of organizing them because by the time I have done organizing the boxes, they would have been up on the self anyway. (So this is wrong? I cannot use 'would' with 'by the time' ? If this is correct, what does it mean?)

3. There is no point of organizing them because by the time I have done organizing the boxes, they would be up on the self anyway. (So this is wrong? I cannot use 'would' with 'by the time' ?)

4. There is no point of organizing them because by the time I have done organizing the boxes, they will have otherwise been up on the self anyway. (Is this one correct? If not, how is 'otherwise' used? Does this sentence have exactly the same meaning as #1? )

With respect to my scenario:

Are both of #5 and #6 correct?

5. There is no point of organizing them. (What does this one mean? I'm referring to boxes with 'them'?)

6. There is no point of organizing it. (If this is correct, what is 'it' referring to? Is 'it' referring to the situation?)

Thanks.
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 Danyoo's reply was promoted to an answer.
Could you also explain my sentences from #1 to #4?

Thanks.