IMO, there is really no reason to boil for 90 minutes with your grain bill and 60 minutes is plenty of time for your mash as well. If you were using a lot of Pilsner malt which can create a lot of DMS, 90 would be preferable. Also, with the amount of darker grains you have be sure your Ph is in the 5ish range. Astringency and tannin extraction can be an issue if Ph is high and you sparge over 170F.
If you are using software be sure your equipment is set up properly to calculate all of your volumes correct. You need to be sure you are properly calculating grain absorption, tun dead space, kettle loss etc. so you get proper efficiency and volume into your primary