Ricardo - Put the water box on your list of things to check that might cause limited RPM, the reason is this valve restricts water flow into the expansion pipe during high throttle like WOT and you will lose RPM if there's too much water being injected into the expansion pipe during WOT. There's a small pintle that moves up and down inside this valve based on the pressure in the water box and the rubber bellows inside the plastic cover should not leak water into the bilge. You can unscrew it from the water box and see if the pintle moves freely or if some sand/debris is jammed inside causing too much water injection to the expansion pipe.
First, I think you should repair the RAVE base o-ring leak, my o-rings are original and they are fairly soft, they don't leak like that, I put about 70in-lbs torque(my estimate) on the mounting screws, not a crazy amount of torque. The o-rings make the seal. I don't think this leak is causing limited RPM but it's hard to know for sure, just about any exhaust leak will fill the bilge with carbon monoxide and cause problems b/c the carbon monoxide displaces air and the engine needs air, carbon monoxide in the bilge pushes combustion air out of the bilge. I think you get the idea.
I guess you didn't over rev the engine b/c you only reached 6250, LOL, maybe you didn't hold throttle WOT long enough to reach top speed (7000 RPM)?
Anyway, I agree, avoid WOT but the engine has to be tested to confirm nothing's wrong that might cause damage.... A chicken or egg thing.
Also check and make sure those throttles are opening completely, this will limit top RPM I think you know. Maybe the throttle cable needs to be adjusted. For adjusting, I pull the throttle to WOT while adjusting full tension on the cable, maybe you know what I mean.
You did good on oiling the motor and not oiling the fuel, it's fuel-injected so you can't oil the fuel. I think you know this too, that's why you didn't.
Check those RAVES carefully, make sure the air tubing is connected and the pneumatic valves can hold air pressure. If the RAVES aren't opening, the RPM's will be limited (I think you already know this too).
For the TPS, maybe the service guy who has the VCK/code reader will reset them for you, we forgot to ask him... I kinda think this isn't the problem right now but it's possible maybe.
I think most likely the RAVES aren't actuating or the waterbox valve isn't moving the pintle, or the throttle cable needs minor adjustment to open the throttle body butterfly plates completely. Checking the throttle cable adjustment is the easiest thing to do first.
And you need to fix any exhaust leaks you can find, those are no bueno.
Nice work, so far so good!