When switching from a 260/alpha to a BB/bravo 1 are the motor mounts the same? I know about the 2 extra holes for the Bravo. Will the stock alpha throttle /shift cables work? How does the alignment work? Will the stock 260 harness work on a 90s BB? Both are carbs.

any/all tips and tricks is appreciated.

Motor Mounts the same
The '86 uses the old style ends on the cables, so maybe. You need to change the shift plate to a Bravo, slightly different swing on arm and no interrupter switch, so you may need to change that cable (shift).
You need an alignment tool, available from ebay about $ 30
Should, there are 2 connectors I am thinking a 9 pin and a 10 pin. Your boat has the 9 pin, if your new motor has the 10 pin, you can remove the motor side connector from your 260 and put it on the 454 and that will work.
Good luck, don't go stock 454 or you will be very sorry very soon.
For the misc parts you need check with OSO member Sick Stinger, he is very helpful with these parts at a reasonable price, he also has motors for sale at a price you cannot build one for.

Thanks for the info. What would this run with a stock 454/B1? The 260 works fine, just would like a little more speed. Yes it's all stock. If it works out I will have under $2300 into the drivetrain. Thought for that it may be worth it.

Yes a LITTLE more speed is what you will get

Here is what Formula said

Exhaust tip location might be off. If using stock exhaust with long hoses, that won’t be an issue. But if you use aftermarket exhaust it could create some problems with exhaust tip alignment.

454... a stock non-mag 330 engine is going to give you low 50’s, high 40’s dependent on load. The 365 mag will get you around 55. If you have a mag, then you have a good foundation to build from.

It's not a mag. If it was low 50's that would be gaining me 10mph. How much heavier is the BB/B1? I like how the boat sets in the water with the SB