Service manager is giving you some fair advice.
1. 12k miles on the motor with that in mind since you have to do a complete tear down and have the heads off have someone do a complete job on the heads, new springs, valves, seals. and port / polish job and flow.
2. Have timken put in but i would go with the 07 style cam plate and not go gear drive
3. Use cam of choice of the head guy. You can increase the compression some, but should stay at 10 to 1 compression or under and get good results without giving up reliablity. John Sachs just did 2 of these that I am familiar with. He is a member on the site here and can comment on the heads or send him a PM.
4. Have the crank balanced etc by Hoban Brothers aka dark horse
5. Would consider the Kuryakins Wild Things over the Rineharts talk to WVultra about sound choices
6. I would use Harley Stock Lifters and not SE Lifters and I would not go with roller rockers unless you choose a cam over .600 lift.
7. Have the porter open your throttlebody up a little to say 48 / 49 mm and continue to use the 4.35 injectors.
Typically these heads in stock form with 253 cams produce 98tq / 94 hp give or take depending on dyno, pipes, tuner with headwork a little compression you can easily produce 115/110 and have a reliable motor.
You will give up some down low power when you go to true duals over a 2 into 1. Just depends on you.
Sorry to hear about your motor but better with warranty than not