From your list the only real non independent "wa/وَ" is in
وَجَدْتُمُوهُمْ
which is a plural form of the verb: وَجَدَ.
In all other posted cases "wa" is an equivalent to "and" and therefore should be considered as a different or independent word. I honestly don't know if there's really any rule saying one should "hang them" on the following word.
But how would you analyze the Quran linguistically if you don't even know which words can be separated and which not? You should first star by learning Arabic and try to know the roots of the words!
I mean if you take away those "wa" you would change the meaning in most cases dramatically, so that the sentences wouldn't make any sense. This would also have major impact on the grammatical rules -assuming there still will be some useful sentences left-.
IMO you should still elaborate your Question or try to explain how you would achieve what you want to do unfortunately I'm not able to follow your link as I'm behind a firewall!
As for why "wa" is so prevalent, one reason for that is the use of many "and's" in the Quran, also a lot of Arabic words start with "wa" as the verb already mentioned above an other frequent example in the Quran is
ويل
then it is used for oaths as described by goldenPseudo for example
in:
وَالعَصْرِ (al-'asr)
or
وَالتِينِ وَالزَّيتُنِ وَطُورِ سِنِينَ وَهَذَا البَلَدِ الأمِينِ (at-tyn)
where 3 of the "wa's" are of this kind (the 2nd one in the order of the verse is an equivalent to "and")!
on the other hand as the letter "واو" in Arabic is one of the letters which appear especially at the beginning of a word like an independent letter. You may miss the fact that in Quran there are many words that start with a "فاء" / "fa ف" or "باء" / "ba ب" or other letters, which aren't a part of the "next" word like:
فَمَا at-tyn
or
in surat a-Shams
فألهمها
فقال
فكذبوه
and in some riwaya:
فلا يخاف instead of ولا يخاف
note that about all the rest of the verses of this surah begin with an oath.
or in surat al-qadr
بإذْنِ رَبِّهِمْ
in surat al-'alaq
بِاسْمِ
بِالقَلَمِ
بِالتَّقْوَى
بِأنَّ
بِالنَّاصِيَةِ
just to give some examples from short surahs.
And Allah knows best!