I've done these peaks from both Navajo and Kilpacker so, if you don't mind one more opinion, I'll throw in my 2 or 3 cents...(I preferred Navajo, BTW):
First Trip:
Navajo Basin camp
North Buttress ascent on El Diente
Traverse to Mt Wilson
Descent back to Navajo Basin
Made an impromptu attempt for Wilson Peak, but ran out of water and headed back to camp
Did Wilson Peak the next day from Navajo Basin camp
Second time (with mtgirl - see her post):
Camped at Kilpacker Basin TH
South Slopes ascent up El Diente
Traverse to Mt Wilson
Descent down to Kilpacker Basin
Drove around to ROA TH
Ascended Wilson Peak from there
Given what you said about your climbing abilities and conditioning, here is my humble opinion:
First and foremost, these are not peaks to be rushed and require much focus. With that being said....
If you are making good time and the weather is perfect, go for all 3 (bring a water filter). Either from a high camp in Navajo Basin or doing the car shuttle from Kilpacker to ROA TH. There are a some bail options into Kilpacker (but not many) along the traverse, if needed or you can bail after Mt Wilson into Navajo or Kilpacker if the weather is turning.
If you are breaking this into 2 trips
I preferred the Navajo Basin side to Kilpacker for El Diente/Mt Wilson duo. The North Buttress route up El Diente was fairly solid and somewhat fun, but care still needs to be taken (we did encounter some loose rocks, but not many). We followed the route description on this site and it was spot on.

I avoided the slabs by going to the right, up an easy class 3 section...I don't like slabs.
When down climbing Mt Wilson into Navajo Basin, it was as loose and steep as they all say. I descended a different gully than the standard route to avoid being in anyone's fall line or having anyone below me and it worked out ok, just very time consuming. And once you are off the loose stuff, you are on a splendid trail.
The routes from Kilpacker, both up El Diente and the descent off Mt Wilson into Kilpacker are the safest options, I agree 100%. I liked the South Slopes route up El Diente and you can avoid down climbing the crux on Mt Wilson, if desired, and descend a class 2+, loose, gully into Kilpacker Basin. This descent gully was less steep and shorter than MW's descent gullies into Navajo Basin and it had fewer people heading down that way.
However, I loathed, absolutely LOATHED hiking out on the miles and miles of endless, wobbly, ankle twisting, knock-you-on-your-butt, cuss-like-a-sailor, talus. It was maddening and never seemed to end.
So granted, the trade off is safety vs. sanity, which seems like safety should always win. However, I (personally) felt that the North Buttress was a "relatively" safe ascent option (for El Diente) and that the descent off Mt Wilson although steeper and longer into Navajo, was also relatively safe (with care) and worth the trade off for the nice trail at the bottom.
As for the traverse, I too vote for the higher traverse over the lower one, but have never done the lower traverse myself. There were many people on the traverse the last time I did it and I would rather be up high if worried about rockfall. I'm sure either one works fine though.
As for which TH for Wilson Peak...not a lot of preference. Found both to be very similar, in enjoyment, scenery, and difficulty. However, you do get to play in the mining car if you come from Navajo.
As I said, this is just my opinion based on my experience.
Have a great trip. I loved these 3 peaks! Yes, even El Diente!