Possible turbo lag
 

Modified the fuel plate and now when I get up to about 40 mph in 4th and 5th gear my rpms shoot up. Was wondering if this is turbo lag or what could cause that?

RPM shoot up - without the truck accelerating means clutch slippage, with the truck accelerating like mad- OK you are on the boost and now drive a Cummins Diesel.

Do not lug your engine in 5th gear, this can damage the transmission, and the diesel hates being lugged.

It is the latter but It seems like I had more power before modifying

More power getting to the ground most likely.
Now when the boost hits you just push the power right through your smoking clutch is what is likely happening.
Your clutch was probably just holding the old power level. Now when it slips, very little power is getting to the rear wheels.

It is easy / cheap to make lots of power with a Cummins motor, being able to use it all is where the work and money spending usually happens.
I like South Bend clutches for the 12V trucks I turn up the power in.

As AlpineRAM said, do not lug your Cummins at low RPM in too high a gear. It is bad for all the driveline.
I like to run at least 1800-2000 RPM if I am more than 1/2 throttle or accelerating.

Getting an upgraded clutch and it will help with the "power loss"?

If I am understanding your problems correctly.
Which seem like free revving and power loss in 4 and 5 gear after installing a fuel plate.
Those sounds like the clutch not being able to hold the new power and slipping, allowing the motor to rev up AND power to not be applied to the ground.

If you are loosing the power through a slipping clutch...than yes it can.
At some point it is not about how much power the engine can make but becomes a question of how can you get all this new found power to the tires.

This is my first time modifying so I'm still figuring every thing out about it. All this is really helpful. If there are any other things you would recommend it would greatly appreciated

Get gauges, at least pyro and boost.

If it's the latter- meaning truck accelerates like mad, it isn't the clutch.

Gauges first, as oliver foster says- always better than to replace an engine.

Does your truck smoke while you try to accelerate or not?
if not: Maybe you did mount the AFC housing further back than before, this would limit your low boost fueling and cause this lag. For grins an giggles slide your AFC housing fully forward, go for a test drive and observe acceleration and smoke level.

There are some threads on AFC tuning.

Any set that is gonna be reliable but not break me

I thought I put it forward but I will check it again to be sure. How much do you adjust that afc wheel?

This depends on what I want to achieve and how the engine is set up.
Take a read in the AFC tuning threads, you'll see a lot of different factors come into play in that system.

But you could answer the smoke question first?

There is no smoke

OK, no smoke means no fuel. Check the AFC, especially housing position. Slide forward until you get a light haze (no coal rolling) at an attempt at snap acceleration. If too much smoke turn starwheel top towards drivers side fender for 10 clicks, write down the 10 clicks and go for test drive. Check again for smoke and responsiveness.

If your starwheel has not yet been adjusted you should try to get a baseline with the housing first, then fine-tune with the starwheel.
Also check your boost reference hose to the AFC for leaks.