The other things that add up in cost are things that should be done anyway IMO. Have the heads reworked, block cleaned, all new bearing etc. I'd recommend an adjustable rocker conversion. You'll also want to go to bigger injectors (28 lbs seems to be a good size), the stock injectors are barely adequate for a bone stock truck.
With bigger injectors the stock system will handle everything you want to do, as long as its tuned correctly.
What year is your truck? If its a 98+ then hp tuners and efi live (i believe?) can be used to tune your truck. If this is the case then the stock computer is adequate, but the 0411 is better. So 0411 swapping is something you may want to read into. If you're 96-97 you'll probably need to 0411 swap, unless you can find a shop that deals in software for the older computers.
No matter what you do (496 vs bore and cam) you'll want some sort of tuning done. If you stay with a bore and mild cam you might be able to get away with a mail order tune, but you'll probably be leaving power on the table.
EDIT: Its a 99, so you can probably get by without an 0411 swap, if you don't want to run down that rabbit hole.
Thanks so much for the advice. The truck is a 99. I talked to a well known engine builder here in Colorado on Monday. His suggestions were similar to what some folks here have mentioned. One thing he was adamant about was that for my uses stroking the motor was not something he would do. As mentioned before you're looking at lots of extra expense like high flow heads and if you want to run EFI some very spendy aftermarket kit. We mostly covered long block ideas during our conversation.
He suggested the following:
1. Keep compression as close to stock as possible, maybe a quarter point bump to keep the efi happy. I need to research the 99 EFI system to see what sort of tuning it can do. Info is a little hard to come by. He's a carb exclusive builder so I need to do some additional research on this.
2. Take the long block to the best shop around with the best machines. Have it blueprinted and put together really well with new long skirt pistons. He mentioned how much power you can pick up by simply reducing friction. Use at least a 1.5-1.5-3mm ring set.
3. Install CHE bronze valve guides and stainless valves. Have the seats recut. Clean up the heads as much as possible and flowed to see where they're at. I've seen some numbers for L29s that isnt bad. He also suggested investing in adjustable roller rockers.
4. He said the stock cam numbers aren't that bad. He's never built an L29 but knew about the 6 degree retard against the crank. The machine shop that will be doing the long block is a COMP dealer and will help me spec something out. This seems like the zone where there is some potential, and something I've read countless times on the web about L29s.
In general is seems like this thing has a super weak tune from the factory. Is that kind of the consensus? I will definitely be adding the stepped up injectors to the parts list.
I suppose the goal at this point is a nicely built, easy running L29 with gobs of low end torque that isn't going to throw a fit if it gets a tank of questionable 87 from some middle of no where gas station.
Just to Summarize where I'm leaning:
Bore & deck block minimally.
Deck head minimally
Flow the head
Bronze guides
stainless valves
Adjustable roller rockers/PR
long skirt pistons (need to spec)
all bearings
Crank polish
Injectors
Stock Manifolds (?)
New cats
4l80E rebuild
ECM Tune
Anything I'm missing?