My shop is in EUR. But for simplicity i have added some products in USD when pricing them.. Works great in the shop in general and price is correct if i make a order from the frontend.
But if i make a order manually it will take the USD price and set it as EUR with out recalculation.
This despite the invoice being set to EUR

issue 2..
why cant i add product with sku anymore when making invoice manually?

The manual order is set simply with the currency and values you enter. No recalculation is being done there.
So if you choose USD as order currency, all prices on it are in USD.

ad issue 2) I am not aware this was possible before - AFAIK the AJAX search was always using a title search; anyway, we may add support for SKU-based search to next release, it is a good idea