IIS config error after upgrading to ASP.NET Core 3.0 from Core 2.2

I upgraded a few if my web projects to asp.net core 3.0 and am trying to push them to an IIS web server. I installed the .net core 3.0 hosting bundle and runtime and uninstalled the old versions just in case.

I tried to load the page but I get the error:

HTTP Error 500.19 - Internal Server Error
The requested page cannot be accessed because the related configuration data for the page is invalid.
Error Code     0x8007000d
Config Error       
Config File    \\?\C:\inetpub\MySite\web.config

Below is my web.config:

<?xml version="1.0" encoding="utf-8"?>
<configuration>
  <location path="." inheritInChildApplications="false">
    <system.webServer>
      <handlers>
        <add name="aspNetCore" path="*" verb="*" modules="AspNetCoreModuleV2" resourceType="Unspecified" />
      </handlers>
      <aspNetCore processPath="dotnet" arguments=".\MySite.dll" stdoutLogEnabled="false" stdoutLogFile=".\logs\stdout" hostingModel="">
        <environmentVariables>
          <environmentVariable name="EXCLUDED_LINE" value="Test" />
          <environmentVariable name="COMPLUS_ForceENC" value="1" />
        </environmentVariables>
      </aspNetCore>
    </system.webServer>
  </location>
</configuration>

Other than the version of .net I haven't changed anything else on the server - I am directly replacing the pervious working projects.

startup.cs:

using System;
using FluentValidation;
using FluentValidation.AspNetCore;
using Microsoft.AspNetCore.Authentication;
using Microsoft.AspNetCore.Authorization;
using Microsoft.AspNetCore.Builder;
using Microsoft.AspNetCore.Hosting;
using Microsoft.AspNetCore.Http;
using Microsoft.AspNetCore.Server.IISIntegration;
using Microsoft.EntityFrameworkCore;
using Microsoft.Extensions.Configuration;
using Microsoft.Extensions.DependencyInjection;
using Microsoft.Extensions.Hosting;

namespace MySite
{
    public class Startup
    {
        public Startup(IConfiguration configuration)
        {
            Configuration = configuration;
        }

        public IConfiguration Configuration { get; }

        // This method gets called by the runtime. Use this method to add services to the container.
        public void ConfigureServices(IServiceCollection services)
        {
            services.Configure<CookiePolicyOptions>(options =>
            {
                // This lambda determines whether user consent for non-essential cookies is needed for a given request.
                options.CheckConsentNeeded = context => true;
                options.MinimumSameSitePolicy = SameSiteMode.None;
            });

            services.AddAuthentication(IISDefaults.AuthenticationScheme);

            services.AddTransient<IClaimsTransformation, CustomClaimsTransformer>();

            services.AddSingleton<IAuthorizationHandler, CheckADGroupHandler>();

            services.AddRazorPages().AddFluentValidation();

            services.AddDbContext<MyContext>(options =>
                options.UseSqlServer(
                    "Data Source=MYSERVER\\SQLEXPRESS;Initial Catalog=MyDB;Integrated Security=True;Connect Timeout=30;Encrypt=False;TrustServerCertificate=False;ApplicationIntent=ReadWrite;MultiSubnetFailover=False"));
        }

            // This method gets called by the runtime. Use this method to configure the HTTP request pipeline.
        public void Configure(IApplicationBuilder app, IWebHostEnvironment env)
        {
            if (env.IsDevelopment())
            {
                app.UseDeveloperExceptionPage();
            }
            else
            {
                app.UseExceptionHandler("/Error");
                app.UseHsts();
            }

            app.UseRouting();
            app.UseAuthentication();
            app.UseAuthorization();

            app.UseEndpoints(endpoints => endpoints.MapRazorPages());

            app.UseHttpsRedirection();
            app.UseStaticFiles();
            app.UseCookiePolicy();

        }
    }
}

project:

<Project Sdk="Microsoft.NET.Sdk.Web">

  <PropertyGroup>
    <TargetFramework>netcoreapp3.0</TargetFramework>
    <AspNetCoreHostingModel>InProcess</AspNetCoreHostingModel>
    <AssemblyName>MySite</AssemblyName>
    <RootNamespace>MySite</RootNamespace>
    <LangVersion>8</LangVersion>
  </PropertyGroup>

  <ItemGroup>
    <PackageReference Include="BuildBundlerMinifier" Version="2.9.406" />
    <PackageReference Include="FluentValidation.AspNetCore" Version="8.5.0" />
    <PackageReference Include="Microsoft.AspNetCore.Razor.Language" Version="3.0.0" />
    <PackageReference Include="Microsoft.EntityFrameworkCore" Version="3.0.0" />
    <PackageReference Include="Microsoft.EntityFrameworkCore.Design" Version="3.0.0" />
    <PackageReference Include="Microsoft.EntityFrameworkCore.SqlServer" Version="3.0.0" />
    <PackageReference Include="Microsoft.Extensions.DependencyInjection" Version="3.0.0" />
    <PackageReference Include="Microsoft.Extensions.DependencyInjection.Abstractions" Version="3.0.0" />
    <PackageReference Include="Microsoft.VisualStudio.Web.CodeGeneration.Design" Version="2.2.3" />
    <PackageReference Include="Microsoft.Windows.Compatibility" Version="3.0.0" />
    <PackageReference Include="NLog" Version="4.6.2" />
    <PackageReference Include="NLog.Targets.Syslog" Version="5.1.0" />
    <PackageReference Include="NLog.Web.AspNetCore" Version="4.8.1" />
  </ItemGroup>

  <ItemGroup>
    <Folder Include="wwwroot\css" />
    <Folder Include="wwwroot\webfonts\" />
  </ItemGroup>

</Project>

I tired putting manually copying it to a test IIS and most pages just show error 500, although I can browse the web.config.

I experienced the issue both on a new server and on a server which I uninstalled core 2.2 before installing 3.0. Eventually I found a server that worked and realised I had forgotten to uninstall the old hosting bundle so it had both 2.2 and 3.0

In the end I fixed it by installing the asp.net core 2.2 hosting bundle on the servers alongside asp.net core 3.0 hosting. Site is now working fine.