AkhkharuXul is absolutely correct. The pulses are for desynchronization and not to prevent engine overheat. Actually, loss of heat from the desynchronization pulses is an unfortunate and unwanted side-effect, which is why I tuned my system to send out pulses as infrequently as possible. Having all the engines hooked up to the same pulse generator is useless, since while they may not overheat in that situation, they stay synchronized (hence the use of an RP2 sequencer).
As for chaining engines together ... I found that in my experiments chaining does not increase bucket extraction rate. Please, if you could, have your friend give you or upload a world file where this phenomenon is observable. Of course, there's the other issue that driving a redstone engine with another 140 engines behind it is going to cause a bunch of your engines to explode anyway.
To answer your question about adding more than four inflow pumps. The reason there's only four is because even a nearly full 5 chamber reactor with 40 Uranium cells only outputs 1740 heat / second. There's no need for more than four inflow pumps since each can supply about 500 heat / second in cooling.
On the bucket loss subject ... BuildCraft is 'leaky' compared to RP2 pneumatics. You absolutely MUST use Obsidian vacuum pipes to recover leaks and losses. The vacuum design is going to be dependent on each individual configuration. If you don't use the reference design *exactly*, then the vacuum recovery system will have to be redesigned from the ground up to match whatever design modifications you make.
Due to the circuit complexity involved in making the sequencer work, my friend and I who are going to use this reactor in our SMP server are not going to be removing RP2 logic from our mod stack (There's simply no room in our base to install the redstone circuitry required to replicate the circuits we have built using RP2 logic). However, I'd be more than happy to give you periodic tips and pointers on how to get your own design off the ground and working without RP2 alltogether. I'm a strong believer in more options and competing designs!