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The word lain is a bit of an oddity. On the one hand, it is the only correct form of the past participle of the verb to lie (in the sense of 'be situated'). On the other hand, it does not sound entirely natural – it has a slightly archaic ring. It is rarely used in speech, in my experience. Even in writing, its use is perhaps a little obtrusive.

What do you think? Would you use lain or laid in the sentence below? Would it make any difference whether you were saying it or writing it?

"I have often lain/laid in bed thinking about it."

Thinking about it, I guess I would go for lain, though it's a awkward sentence to me, so I have to force myself to say it.

If I were to say it without thinking about it, I can't guarantee that I wouldn't come up with laid. Hard to not think about it under the circumstances, though.

"Lain" is the grammatically correct choice in your example. In a sentence like the following, I am fairly confident I would come up with "lain"
If it weren't for the mosquitos, I would have lain on the beach working on my tan all afternoon.

And in the following I would use "laid"
Now where have I laid my pencil?

Away in a manger
No crib for a bed
The little Lord Jesus
Laid down his sweet head

'Laid' is correct – it is transitive – but I am sure many people sing 'lay' (although the difference in pronunciation is very slight).

I wonder, however, about a later verse of the hymn:

Be near me, Lord Jesus
I ask you to stay
Close by me for ever
And love me, I pray

The syntax seems rather odd here. If we assume that "I ask you..." starts a new sentence, how does "I pray" fit in? The sentence seems complete without it. Or does "And" start another new sentence?

Does standard syntax even apply here? Wouldn't poetic license allow for many different readings, and placings of commas and periods? Is there an original "true" version of the punctuation?

As quoted, it doesn't have a period at the end. Could "I pray" go with the next line?