Glad this recipe has inspired your first partial mash brew!
I would not use the CaraRed at all. That puts your total crystal/cara malts at 2.25 lbs in a 5 gallon batch. WAY too sweet in my opinion. The IRA has been judged by about a dozen BJCP certified judges and the only consistent critique has been too much crystal/cara malts, and this is with the original recipe with 1.25 lbs. I have notched it down to 1 lb total, and it is better that way- earned 43 points last time.
The way you have the recipe, at 92 IBU, you are going to have a very different beer than the IRA recipe here, but may be great. 90 minutes and 60 minutes are not going to change much. At 90 min you will lose any Citra character at all, but keep the IBU's. If you use it at 60 min, there may be a very slight flavor of the hops remaining. I know from using Simcoe as a solo hop at 60 min in a blonde ale, that you can taste it...just barely in the finished beer.
I would not recommend mystery hops at the end of boil if one of the hops could be Nugget. I have grown Nugget for years, and try as I might to like that hop as an aroma hop, I cannot stand it. Very strong herbal notes that I think are distracting in most cases.
Here is what I would do, (if you have not already brewed!)
1. get rid of the carared, or use no more than 1.25 lbs crystal/cara malts total.
2. no mystery hops-if you can determine that you have Simcoe, use for dry hops.
3. Chill to 65f if you can
4. decrease the dark malt from 4 oz to 1 or 2 oz.
Now, of course this is homebrewing and you may have an amazing recipe there that flies in the face of all of my suggestions