Tim, as the marriage was in Patrick it might not have been attended by Elinor's family from German, and witnesses could be cousins/uncles or other relatives of John's (or not). Did Thomas have a brother John?
Elinor's age was given in the 1851 census as 48 - b.c.1803, which was consistent with her age at burial which was 52 in 1855. I think your first choice of parents for her was far more likely to be correct: bapt. 6 Feb.1803 Kirk German daur of Charles SHIMIN & Elinor COWLL.
The LDS film for German is no. 0106723 [1760-1856] and it should also have John & Elinor's younger children's bapts, plus burials.

John Shimmin's age is consistent in the censuses as b.c.1795, in Patrick, where there were two possible bapts. Now that you have the par reg film it would be well worth looking through it to see whether additional details were given for the bapts of the two John entries and for their siblings, so that you can separate the families - also check family burials. John SHIMIN bapt 28 March 1794 Patrick son of Thomas SHIMIN & Margt CRAIN as well as John bapt 2 Oct 1796 Patrick, son of Philip SHIMMIN & Cath QUINE.

As well as looking through the register those two wills could be a huge help in sorting them out:
SHIMIN, Margaret buried Patrick 31 May 1817
Will: SHIMMIN, Margret 1817 Pat E 2 [LDS film no.] 0106419
This has a 50% chance of being the right one (other Margt Shimmin buried 1823 - the 1842 one was not Thomas's wife).
Also:
SHIMMIN, Philip Patrick 28 Jun 1822
Will: SHIMMIN, Philip 1822 Pat E 2 [LDS film no.] 0106423.

I think you are probably right that Thomas was John's father, and that he was the witness, but it would be good to have more supporting information.

Sue