It just so happens that I was preparing a slide on this for my next debate, here it is:
Single Nucleotide Polymorphism(1) ~3%(of 76% that is alignable)
Insertion/deletion(1) 1.2%(of 76%)
Total difference about 30%
3PLoS ONE 1:e85
I have been checking these references, or at least trying to. The last has so far eluded me as insufficient information is provided for the last one. The PLoS ONE site seems not to lend itself to searching by volume or page numbers. Please provide more information, or (better) a link.
The second deals with duplications, and concludes with:
"Nevertheless, when compared to single-base-pair differences, which
account for 1.2% genetic difference, base per base, large segmental
duplication events have had a greater impact (2.7%) in altering the
genomic landscape of these two species."
Note this is on a base per base basis. As one duplication will duplicate many bases, it will have a disproportionate effect. It would be more reasonable to count a duplication as one difference, on a par with a single base pair change.
A similar argument applies to indels, which again affect multiple base pairs. They should, therefore, be seen as one difference each, instead of multiple differences (multiple differences would mean each base pair difference being individually counted). The ca. 3 % of base pair differences caused by indels then becomes about 0.4 % difference, as indels are about 7 times less common than single base pair changes. Add this on to the 1.2 % difference due to single base pair changes and we have 1.6 % difference, plus the difference from duplication events, which as I explained above may be much, much less than 2.7 % if one counts duplications as single differences. An overall difference of 98 % may be quite reasonable.
I can find no mention of your "Non-alignable(1) ~24%" figure in either of these Nature papers. Please provide precise details - page number, column, paragraph. I'm not sure that this figure is meaningful anyway. It only takes one base pair difference to render a sequence of DNA non-alignable. It is a bit like declaring a whole page non-alignable with the corresponding one in another edition of a book because one single letter is missing, thereby throwing the whole sequence out by one. The authors also comment that "nearly all of the bases are identical by descent and sequences can be readily aligned except in recently derived, large repetitive regions."
The authors of these papers do not consider human and chimp DNA to be radically different, and certainly not by 30 %. Indeed they conclude with an affirmation of our striking similarities:
"We hope that elaborating how few differences separate our
species will broaden recognition of our duty to these extraordinary
primates that stand as our siblings in the family of life."
See also http://www.talkorigins.org/indexcc/CB/CB144.html
for a brief summary of the importance of keeping to a consistent method of counting genetic differences, and that if you do this then chimps come out as our closest relatives. It looks to me like you are trying to fiddle the figures to ramp up the differences as much as you can. A standard creationist ploy of distorting the evidence to make it fit.
I think you will need to change your slide, or (better) ditch it altogether.