That's too many IP, first of all. At $255M I almost exclusively use Coors Field and rarely draft more than 1850 IP. You can always draft extra to be safe, but I've rarely ever had pitching fatigue issues with those kinds of IP totals. You could use even less IP at pitcher's parks.
Second, WHIP and ERA are not used in the SIM to determine the outcome of any actual game event. I wouldn't even bother to look at ERA at all as it means nothing in the SIM. WHIP is useful as a comparison tool as it's a good measure of a pitcher's overall effectiveness in terms of OAV and BB, but WHIP itself is not used in SIM calculations. I focus on OAV (weighted by OAV+ when comparing similar pitchers), BB/9, and of course HR/9. At any cap, you're basically trying to assemble a pitching staff with the best combination of OAV, BB/9, and HR/9 within league parameters. Those are the "Big 3" that primarily affect the outcome of an AB in the SIM.
Another thing to keep in mind is that even the best pitcher seasons of all time will likely produce ugly-looking numbers at high caps. As long as your staff's numbers are less ugly than your opponents' though, you'll be fine on the pitching side.