I think you took the appropriate next step in requesting an IEE, so I would just wait to hear back from that. They will most likely grant it, as otherwise they have to take you to due process. If they don't, this is probably something you could handle without an attorney since the only issue is getting an IEE. Reach back out to this forum if you do have to go to due process over this.
If your request is granted, make sure the IEE is done in ALL areas that the school evaluated and that you disagree with. (If the school has not evaluated in all areas of suspected disability, ask them to.) As Jenna alluded to, hopefully the IEE will tie his disabilities to academic impact.
Do NOT accept grades as data - they are not. Grades are very subjective and should not be the basis for denying eligibility. I don't know how old you son is, but this is especially true at the elementary school level. Request that they redo the Prior Written Notice in which they explained their reasons for denying eligibility and ask for DATA that they relied on - not grades. In the area of speech, it sounds like they won't have any, so the only thing they can look to (until the results of the IEE are in) is your private evaluation.