The previous thread (link above) offers a fair bit of information. Spend 5 minutes and read it through, for a better idea what's involved.
To answer your questions, moving the helm aft a little isn't going to upset the boat, as it was designed to handle folks sitting on the aft seat anyway. The console doesn't weigh enough to be overly concerned about and on the centerline is better balanced, so unless you plan on three 400 pounders in the aft seat, you'll be fine.
The images aren't clear enough to tell what's going on, but one thing is obvious, the structural framing is too widely spaced to be effective. No gussets, stringer and support bonding directly to the hull shell and likely a lousy fastener schedule of dubious type, all contributed to movement between the hull shell and the wooden elements of the structure. This movement slowly, but surely caused the fasteners to pull out and work loose in their holes, introducing more movement and localized load tasking took place, which just breaks stuff. You see, the idea with this type of structure is to have all the parts, bits and pieces help share and transmit loads, so no one or two pieces, have to do all the work. This permits smaller (read lighter and less costly) structures to be installed, but if the structure develops weak points, because of fastener and bond break down, surrounding structural elements have to accept, the now dramatically increased load transmissions (read crap breaks).
Those athwart supports look to be on 48" centers, which is way too much. Decrease this to 24". The longitudinal stringers appear to be on 16" centers and this is also a bit wide, assuming they used skinny plywood (3/8") for the decking. You can use 16", but evenly space them across the beam AND use slightly thicker plywood for the decking. If weight is an issue, use a 12" - 14" spacing (again evenly) and the same thickness plywood as previously employed. It's usually lighter to use a slightly more closely spaced support system (stringers and athwart braces) than to use thicker plywood.
If using Lowe's/Depot plywood for the decking, use two layers of 1/4" underlayment, instead of 3/8". You'll glue and screw this together, staggering the seams, as you go. The reason for this is the quality of this type of plywood (big box stuff) isn't great, so you can increase the veneer count by doubling up the decking, making a stiffer sole (what the plywood actually is).
Lastly, use screws to hold the decking and structural elements together, not nails or staples. Stainless is the way to go and yeah they do cost a good bit more, but they'll be buried in the boat, where you can't get at them, without tearing things up again. Technically, if you use good epoxy procedures, you don't need the fasteners, but if you're a belt and suspenders guy, toss in some screws or through bolts.