As someone who has built 8 Nitro RS4s over the years, including one with a 3.4cc engine shoved into a smallblock form-factor, I can confidently tell you that 5.9cc is MASSIVELY overkill for that chassis. The chassis will be dangerously unbalanced with an engine that large, and the tires won't be able to stick that much torque to the ground anyway. You're probably imagining something like stuffing a LS1 into a Miata, but it's actually more like stuffing a LS1 into a go-kart -- it's more power than the platform can possibly use, it will handle like shit, and you WILL crash it.
The stock 3.0cc engine has more than enough power unless you're trying to go above 60mph, and in that case you're better-off buying a higher-end smallblock engine like an OS 21TM. It will outperform that 5.9 engine in the way that a touring car actually needs -- high RPM and top-end power. Truck engines provide monster torque, which is useless for touring cars.
If you just want to get the car up and running again, any pullstart engine from 2.1-3.4cc (aka .12-.20 cubic inches) -- even cheap no-name Chinese engines -- will work just fine. Just buy one on eBay and save yourself the pain of what will ultimately be an extremely difficult custom job with disappointing results.